Those annoying gaps are in regular Amnesia too.

[Cranky Old Man]

I think I actually spotted this in-game, noticing that I could see into the roof of the dog room, and then spotted the gap again just now. As a perfectionist, I'll try to use the wooden extension walls with these ceiling corners instead.

Edit: Wtf? The extension walls don't go all the way up to the next section. Sure, you can take the grid off and fine tune all the roof sections, but it looks like I'm only going to use the white walls with the white ceiling corners.

Edit 2: ...and those wall sections with hidden alcoves behind the paintings, they're actually a pixel too narrow, even if you place them with maximum (three) decimal precision, and the reason why those gaps doesn't show in-game, is because the wall section is in a corner. I can weld the gap with a pillar, but that might look a bit conspicuous.