I’m trying to create NFTs. When I save layers, each layer keeps the canvas in the background even when I save it with the background unchecked. Another problem is that I have 50x50 pixel art but the saved file always has a stretched frame (greater than 50x50 and it off centers the pictures).
Another thing I noticed is that when I set frame to document or set frame to layer, It changes the frame to 64x64. This is how the files save but I wan’t them saved as 50x50.
Regarding transparent background, have you unselected “Show background” in the View menu?
As for specific sizes, MyPaint is mainly focused on painting and less on image editing. I too have found the border thing to be less than exact. Your best option is probably to open the image in Krita or Gimp and do the cropping there.