The solution for Topological Naming Problem (TNP) was merged just before the 1.0 release. A lot of other significant changes were also merged in at the same time. Some people have reported that the UX has improved a lot since then.

I don't know much about the internal architecture of FreeCAD. As far as I know, FreeCAD does a lot of heavy lifting including managing TNP. It's supposed to be handled by the CAD kernel - OpenCASCADE in this case. I suspect that the reason why open source CAD lags behind their proprietary counterparts is really the CAD kernel. Many proprietary CAD software share the same kernel, in fact. For example, SolidWorks, Solid Edge and OnShape use Parasolid. It tells you how critical the kernel is.

Perhaps we should be focusing more on a more capable open source CAD kernel. There are a few projects around that are trying this. But they either have very limited scopes, or don't have enough support and momentum.