Any one know how to make a restart button?

Great idea! I've programmed it so that the Start button reappears together with the Game Over message, but with Restart on it:

gameOver(message) {
        const gameOverBox = document.getElementById("game-over");

        gameOverBox.style.display = "block";
        gameOverBox.innerHTML = message;

        beginGameButton.style.display = "block";
        beginGameButton.textContent = "Restart";
    }

Then I've added the function Eric suggested to the beginGameButton event listener like this:

beginGameButton.addEventListener('click', function() {
    if ( beginGameButton.textContent.trim() === 'Start' ) {
        game.startGame();

        this.style.display = 'none';
        document.getElementById('play-area').style.opacity = '1';
    } else if ( beginGameButton.textContent.trim() === 'Restart' ) {
        window.location.reload();
    }
});

Like this you will need to click the Start button again though. Does anyone have a better idea?

JavaScript has an easy way to trigger a page refresh. It's:

window.location.reload();

So you could add that to a button's click event handler, like so:

// Let's say your HTML has <button class="restart-btn">Restart Game</button>

document.querySelector('.restart-btn').addEventListener('click', function(){
  window.location.reload();
  return false;
});

If you don't want to press the start button again, I created a restart button and used the same css styling for the start button except I set the display to none (or just use Birthe's idea to rename the start button). I added this listener to reset the game and create a new game:

 document.querySelector('#restart').addEventListener('click', e => {
    game.reset();
    game = new Game(); // instantiate a new game object to reset values
    game.startGame();
    e.target.style.display = 'none';
});

And added this reset method to Game.js

    reset() {
        let tokenElements = document.querySelectorAll('.token'); // get all token html elements for removal
        tokenElements.forEach(token => {
            token.remove();
        });
        document.querySelector('#game-over').style.display = 'none'; // remove the game over message
    }

If you want to keep score using this way, you'd have to do so from app.js since a new game is created with each reset.