It's a hacky script I programmed in C++. Basically, it generates cubes and glues them together in a pre-defined way.
there are ~5 stl files, each containing a different model - they all have a different color
Not sure what you mean. They are supposed to touch each other's walls (they share coordinates), but nothing is supposed to intersect. I'm using RMB->"Merge Models" to put them in position.
I installed the extension and messed around with it:
The models are not watertight (Which, looking at my code, should be impossible - I guess It's because I ignored wrong-side vertices?)
"Fix simple holes" responds with "The mesh needs more extensive repeair to become watertight"
"Fix model normals" "randomizes" locations of red vertices, but does not remove them (picture):