Those annoying gaps are in regular Amnesia too.

[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.