if you apply paint to the area that you drew with a pencil, it will not be completely painted over

Well you can say, but paint in Windows has the same behavior, I'll say no

Start by reproducing the issue in the Drawing app on Linux: draw an area with the pencil, then apply paint over it and compare the result with the expected coverage. Investigate the drawing and paint behavior to identify why pencil-drawn pixels remain visible; done means the painted area is completely covered.

Written by the indexing model from the issue text.