Hi beetle, it's probably due to the bottom shapes on your first example, the "tubes" part at the bottom don't come to a common flat plane with the main body, each little tube has a just slightly angled surface at the bottom, here is a zoom in to the bottom area:




Things that are overlapping but at shallow angles to one another can tend to create a complex intersection since there will be a kind of partial area of overlap between the pieces (within tolerance) but not a complete overlap. Intersection curves in that kind of shallow case can end up kind of wandering around all over the place and that tends to make for problems gathering up distinct boundaries and partitioning areas cleanly.


Probably the easiest thing is to stretch the tubes out a bit so they don't end right near the end of the main body, let the tubes go a ways past the end and that would probably help avoid some of the most difficult to handle area. If you did want to have the tubes end right there you would want the bottom of the tubes to be more precisely flat so that it would overlap more fully with the bottom face of the main body rather than at a slight angle.

- Michael