Those annoying gaps are in regular Amnesia too.

[Cranky Old Man]

If you play the original Amnesia again, and go to the Study level (with the dog autopsies), walk up to one of the convex corners in the beginning of the level, and look up into it. You'll be staring into space.
Convex corners where "corner_convex_short" and "welder02_convex" are involved, don't work seamlessly together. You'd think that you could cover it up with one of the pillars, but you'd be wrong, because the pillar is cut into by the pillars of the wall (unless you make it reeeally fat), and looks notably brown (while the walls are red) and the concave pillars don't reach high enough, and would look weird if streched. The best solution is probably to take a small plane with the "plane_black" texture, turn it up-side-down, and seal the gap.

[Putmalk]

I would never have noticed it unless you said something, so I don't think it's that big of a problem. There are gaps like this all the time in regular Amnesia; I have the machine room map open right now, look at the ceilings when on the staircase, parts of the transition between the floors open up into space. However, since the maps are usually so dark, the void isn't that big of an issue unless you focus in on it. I would believe almost nobody saw this or cared about it in their playthrough.

[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.

[Putmalk]

Alright, I just don't think it's that big of an issue. If you add scripted events and sounds to the game, I'm sure the player will be immersed enough not to care. XD