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.
There's this https://www.windowsphoneinfo.com/threads/why-does-resizing-m... (made confusing by the next person talking about Paint 3D, a different application) and this https://learn.microsoft.com/en-us/answers/questions/3991946/... (made confusing by the person being an artist and talking in peanut butter metaphors).
But I've only used the program for less than 5 minutes, so maybe it's configured differently?
I don't know why you are so concerned, but it's incredibly easy to test these questions if you really want to know.
The point of paint is a tiny pixel editor. If you want layers there are better programs.