Here is my review. First of all, sorry about it. There is no bug and I can't just read a screen output correctly. It was easier after running your code on my computer than on the post snippet ;)

Just two minor comments.

1. HELPER FUNCTIONS

Those functions are great, but you may want to move the thresholds in the arguments too, so that you could use the same methods for various objects and various analyses. Of course thus won't change anything.

2. REMOVALS

I saw no real value in keeping vectors containing overlapping objects, so RemoveOverlap() works on the vectors provided as its arguments.

This is very correct.