こちらのページで電子ピアノの鍵盤の配置を変えた際、hover (鍵盤の上にマウスを移動させたときに色が変わる) と active (鍵盤を押したときに色が変わる) の効果を外しました。HTML の子要素である黒鍵に対する hover と active の効果を、親要素である白鍵の hover と active の効果から切り離すことができなかったためです。
こちらのページを参考に、白鍵と黒鍵の関係を親子関係ではなく sibling (兄弟姉妹) の関係にして、白鍵と黒鍵の hover と active 効果を切り離しました。
1. JavaScript の主な変更点 (鍵盤の HTML を生成するコードを変更)
下記のコードのように class 属性が key-set-parent の div 要素の子要素として、白鍵と黒鍵のペアを用意することにしました。ピアノの鍵盤を左の鍵盤から順に配置していき、白鍵の右に黒鍵があるド、レ、ファ、ソ、ラの白鍵のときだけ白鍵と黒鍵の両方を class 属性が key-set-parent の div 要素の子要素として追加します。ミ、シのときは、白鍵のみ class 属性が key-set-parent の div 要素の子要素として追加します。
        for (let i = 0; i < keyList.length; i++) {
            const keySetElem = document.createElement("div");
            keySetElem.className = "key-set-parent";
            const whiteKey = keyList[i];
            const whiteKeyName = whiteKey[0];
            const whiteKeyElem = createKey(whiteKeyName, idx, whiteKey[1], 'white-key');
            keySetElem.appendChild(whiteKeyElem);
            if ( whiteKeyName === 'ド' || whiteKeyName === 'レ' || whiteKeyName === 'ファ' ||
                 whiteKeyName === 'ソ' || whiteKeyName === 'ラ') {
                const blackKey = keyList[++i];
                if (blackKey != undefined) {
                    const blackKeyName = blackKey[0];
                    const blackKeyElem = createKey(blackKeyName, idx, blackKey[1], 'black-key');
                    keySetElem.appendChild(blackKeyElem);
                }
            }
            octaveElem.appendChild(keySetElem);
        }
        keyboard.appendChild(octaveElem);
    });
2. cssの主な変更点
下記のように白鍵と黒鍵のペアを格納する親要素の class セレクター key-set-parent を用意します。display プロパティで inline-block を指定し、指定したサイズのHTML要素が水平方向に配置されるようにします。key-set-parent のサイズを指定する width と height は白鍵のサイズと同じです。
.key-set-parent {
    position: relative;
    display: inline-block;
    width: 40px;
    height: 120px;
}
3. 修正後のコード全体
3.1. css
<style type="text/css">
.container {
    overflow-x: scroll;
    overflow-y: hidden;
    width: 100%;
    height: 180px;
    white-space: nowrap;
    margin: 10px;
}
.keyboard {
    width: auto;
    padding: 0;
    margin: 0;
}
.key-set-parent {
    position: relative;
    display: inline-block;
    width: 40px;
    height: 120px;
}
.key {
    position: relative;
    cursor: pointer;
    font: 10px "Open Sans", "Lucida Grande", "Arial", sans-serif;
    border: 1px solid black;
    border-radius: 5px;
    width: 40px;
    height: 120px;
    text-align: center;
    box-shadow: 2px 2px darkgray;
    display: inline-block;
    margin-right: 3px;
    user-select: none;
    -moz-user-select: none;
    -webkit-user-select: none;
    -ms-user-select: none;
}
.key.black-key {
    position: absolute;
    background-color: #000;
    color: #fff;
    width: 36px;
    height: 80px;
    top: 0px;
    left: 22px;
    z-index: 1;
    pointer-events: auto;
    vertical-align: top;
}
.key div {
    position: absolute;
    bottom: 0;
    text-align: center;
    width: 100%;
    pointer-events: none;
}
.key div sub {
    font-size: 8px;
    pointer-events: none;
}
.key:hover {
    background-color: #eef;
}
.key.black-key:hover {
    background-color: #778;
}
.key:active {
    background-color: #000;
    color: #fff;
}
.key.black-key:active {
    background-color: #fff;
    color: #000;
}
.octave {
    display: inline-block;
    padding: 0 6px 0 0;
}
.settingsBar {
    padding-top: 8px;
    font: 14px "Open Sans", "Lucida Grande", "Arial", sans-serif;
    position: relative;
    vertical-align: middle;
    width: 100%;
    height: 60px;
}
.left {
    width: 50%;
    position: absolute;
    left: 0;
    display: table-cell;
    vertical-align: middle;
}
.left span, .left input {
    vertical-align: middle;
}
.right {
    width: 50%;
    position: absolute;
    right: 0;
    display: table-cell;
    vertical-align: middle;
}
.right span {
    vertical-align: middle;
}
.right input {
    vertical-align: baseline;
}
</style>
3.2. HTML
<div class="container">
    <div class="keyboard"></div>
</div>
<div class="settingsBar">
    <div class="left">
        <span>Volume: </span>
        <input type="range" min="0.0" max="1.0" step="0.01" value="0.5" list="volumes" name="volume">
        <datalist id="volumes">
            <option value="0.0" label="Mute">
            <option value="1.0" label="100%">
        </datalist>
    </div>
    <div class="right">
        <span>Current waveform: </span>
        <select name="waveform">
            <option value="sine">Sine</option>
            <option value="square">Square</option>
            <option value="sawtooth">Sawtooth</option>
            <option value="triangle" selected>Triangle</option>
            <option value="custom">Custom</option>
        </select>
    </div>
</div>
3.3. JavaScript
<script>
const audioContext = new (window.AudioContext || window.webkitAudioContext)();
let oscList = [];
const keyboard = document.querySelector(".keyboard");
const wavePicker = document.querySelector("select[name='waveform']");
const volumeControl = document.querySelector("input[name='volume']");
let noteFreq = null;
let customWaveform = null;
let sineTerms = null;
let cosineTerms = null;
const note_names =
[
    ["ラ", "", "A", ""],
    ["ラ#", "シ$\\flat$", "A#", "B$\\flat$"],
    ["シ", "","B", ""],
    ["ド", "","C", ""],
    ["ド#", "レ$\\flat$","C#", "D$\\flat$"],
    ["レ", "","D", ""],
    ["レ#", "ミ$\\flat$","D#", "E$\\flat$"],
    ["ミ", "","E", ""],
    ["ファ", "","F", ""],
    ["ファ#", "ソ$\\flat$","F#", "G$\\flat$"],
    ["ソ", "", "G", ""],
    ["ソ#", "ラ$\\flat$", "G#", "A$\\flat$"]
];
setup();
// -------------------------------------------------------
// functions
// -------------------------------------------------------
function createNoteTable() {
    let noteFreq = [];
    for (let octave = 0; octave < 9; octave++) {
        noteFreq[octave] = [];
    }
    for (let n = 0; n < 88; n++) {
        const frequency = getAudioFrequency(n);
        let octave = parseInt(n/12);
        if (n % 12 >= 3) {
            octave++;
        }
        const note_name_sharp_japanese = note_names[n % 12][0];
        noteFreq[octave][note_name_sharp_japanese] = frequency;
    }
    return noteFreq;
}
function getAudioFrequency(n) {
    return 27.5 * ( Math.pow( Math.pow(2, 1/12), n) );
}
function setup() {
    noteFreq = createNoteTable();
    noteFreq.forEach(function(keys, idx) {
        const keyList = Object.entries(keys);
        const octaveElem = document.createElement("div");
        octaveElem.className = "octave";
        for (let i = 0; i < keyList.length; i++) {
            const keySetElem = document.createElement("div");
            keySetElem.className = "key-set-parent";
            const whiteKey = keyList[i];
            const whiteKeyName = whiteKey[0];
            const whiteKeyElem = createKey(whiteKeyName, idx, whiteKey[1], 'white-key');
            keySetElem.appendChild(whiteKeyElem);
            if ( whiteKeyName === 'ド' || whiteKeyName === 'レ' || whiteKeyName === 'ファ' ||
                 whiteKeyName === 'ソ' || whiteKeyName === 'ラ') {
                const blackKey = keyList[++i];
                if (blackKey != undefined) {
                    const blackKeyName = blackKey[0];
                    const blackKeyElem = createKey(blackKeyName, idx, blackKey[1], 'black-key');
                    keySetElem.appendChild(blackKeyElem);
                }
            }
            octaveElem.appendChild(keySetElem);
        }
        keyboard.appendChild(octaveElem);
    });
    document.querySelector("div[data-note='ファ'][data-octave='5']").scrollIntoView(false);
    sineTerms = new Float32Array([0, 0, 1, 0, 1]);
    cosineTerms = new Float32Array(sineTerms.length);
    customWaveform = audioContext.createPeriodicWave(cosineTerms, sineTerms);
    for (i = 0; i < 9; i++) {
        oscList[i] = {};
    }
}
function createKey(note, octave, freq, keyColor) {
    const keyElement = document.createElement("div");
    const labelElement = document.createElement("div");
    if (keyColor === 'black-key') {
        keyElement.className = "key black-key";
    } else {
        keyElement.className = "key";
    }
    keyElement.dataset["octave"] = octave;
    keyElement.dataset["note"] = note;
    keyElement.dataset["frequency"] = freq;
    labelElement.innerHTML = note + "<sub>" + octave + "</sub>";
    keyElement.appendChild(labelElement);
    keyElement.addEventListener("mousedown", notePressed, false);
    keyElement.addEventListener("touchstart", notePressed, false);
    return keyElement;
}
function playTone(freq) {
    const osc = audioContext.createOscillator();
    const volume = volumeControl.value;
    const gainNode = audioContext.createGain();
    gainNode.connect(audioContext.destination);
    gainNode.gain.setValueAtTime(0, audioContext.currentTime);
    gainNode.gain.linearRampToValueAtTime(volume, audioContext.currentTime + 0.05);
    gainNode.gain.linearRampToValueAtTime(0, audioContext.currentTime + 1.00);
    osc.connect(gainNode);
    const type = wavePicker.options[wavePicker.selectedIndex].value;
    if (type == "custom") {
        osc.setPeriodicWave(customWaveform);
    } else {
        osc.type = type;
    }
    osc.frequency.value = freq;
    osc.start();
    osc.stop(audioContext.currentTime + 1.00);
    return osc;
}
function notePressed(event) {
    const dataset = event.target.dataset;
    const octave = +dataset["octave"];
    oscList[octave][dataset["note"]] = playTone(dataset["frequency"]);
}
</script>