I’ve experienced similar problems (not totally sure if they were exactly the “topological naming problem” but certainly similar from the description) in Solidworks many times. Not usually a major problem - just a reworking or removal / re-adding of some features needed.

I’ve not encountered the same issue in FreeCAD 1.1 (to which I’ve transitioned recently). There are of course other frustrating niggles in FreeCAD, but not this one (yet).