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The topological naming problem is handled quite well by realthunder’s FreeCAD Link Branch fork, and his Assembly3 workbench is an acceptable, albeit imperfect method of making assemblies when combined with his fork. Assembly3 can run on upstream FreeCAD but I found it to work way less consistently due to issues like the topological naming problem breaking links in the assemblies.
Nonetheless the added features by Ondsel look interesting. I’d consider switching once upstream FreeCAD implements a solution to the topological naming problem, but like you mentioned, toponaming is such a huge leap in usefulness that I’m hesitant to switch to another FreeCAD version that doesn’t handle it well.
I haven’t used all of the assembly workbenches but I’ve found Assembly3 to be pretty robust to design changes if you use realthunder’s Link Stable fork of FreeCAD. I wouldn’t be surprised if all of the assembly workbenches would benefit from toponaming fixes, though I don’t know how they all work.