Yeah, I've likewise always figured the reason these reconstructions ended up looking so awful is because paint is generally applied in layers (even to this day), so what they're likely reconstructing is the primer layer.

Like we know from Roman frescoes[1] and mosaics[2] that they were pretty skilled painters and solving the problem of how to paint something to have more hues than a King's Quest 3 sprite is unlikely to be an unsolvable aesthetic problem.

[edit] Changed from Secret of Monkey Island since that game has too many versions and remakes.

[1] https://upload.wikimedia.org/wikipedia/commons/6/6e/Chiron_i...

[2] https://en.wikipedia.org/wiki/Plato%27s_Academy_mosaic#/medi...