I remember when I was doing pixel art, there were some purists that insisted that using layers and transparency/opacity to create windows for your buildings is more or less cheating. According to them, one should manually figure out what the color palette should be for things seen through a window.
Anyway, I continued using layers and transparency/opacity. Pixel art was hard enough already for me, so I didn’t feel that it made sense to artificially make it even more difficult for myself at the time. I had enough other aspects of pixel art to work out already in order to try to get better at it.