Similar problem exist with paving. Lets say You build diagonal road or got one extra here or there.
Now lets remove 1x1 concrete tile and i got 3x3 scorched earth that replaces my paving.
Removing assemblers with central point on native ground, also mess user paving. This also holds for labs, tanks and probably everything 3x3.
Cannot reproduce behavior with 2x2 furnaces, steam engines, refineries, big modded buildings.
Overall brilliant mod. Much better executed than Dirt mod or feature from Natural Expansion.