Now that I'm on Linux, I use jspaint.app.
I would use kolourpaint but for whatever reason overlaid GUI elements like the selection box and brush cursors leave trails on the canvas.
Fun anecdote, paint.exe crashed the other day just as I was finishing up my drawing of the tower of Babel.
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.
The point of paint is a tiny pixel editor. If you want layers there are better programs.
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).
There's some suggestion there that shapes (including lines) are separate entities from pixels. Wikipedia references a now-deleted answers.microsoft.com version of the first question https://web.archive.org/web/20250203164656/https://answers.m... with a couple of people saying that resize is useless. Wiki also says "re-copied" images blur, which is why I wondered if that meant pasting. Also this: https://learn.microsoft.com/en-us/answers/questions/5673783/... a complaint that the tool for drawing pixels doesn't indicate exactly which pixel it will draw to.
But I've only used the program for less than 5 minutes, so maybe it's configured differently?
[^1]: https://lawsofsoftwareengineering.com/laws/zawinskis-law/