Given that extras are deep inside the metadata, I can see the appeal of the latter approach. It means that C remains a single node in the dependency graph, regardless of the extras that are specified. However, it does lead directly to all the issues we’re seeing here (removing extras, conflicting extras (as opposed to merely conflicting requirements)).
Maybe I’m not understanding, so can you explain what “conflicting extra” means? I can understand conflicting version specifiers, but not conflicting extra. From my POV, having C[e1] and C[e2] as separate dependencies automatically means installing C[e1,e2]. Where is the conflict in that?