It's not just a matter of the paint. The point is to machine the ends of the BB shell perfectly square, so that when the cups are screwed in, they are perfectly perpendicular to the spindle. To properly face a bottom bracket shell, you turn the facing tool until any paint is removed, and then continue turning until there is fresh even metal all the way around. Might take a half a turn, might take 3. Stop. Many BB shell were surprisingly uneven on the ends.

For a cartridge BB, removing paint is enough.