Well, as I had discussed earlier with @Geoffers747, this was more of a summary thread to link to all issues that are interrelated like this, … but I guess it could work just as well as a bug report on its own.
A new instance of this that I’ve noticed is when making a flat roof on a building. At least in the building designer (I have yet to actually build such a house), it appears that the roof is one voxel too low, such that the top of the wall overlaps the actual roof.
32:44.
Also thanks to @Krovikan for making me first notice this with his video (15:53):