Its a tricky issue but the sooner you get major changes like this in there the sooner everyone can be on the same page, your suggestion is a fix and shouldnt be treated like a regression! I know it creates extra work but Epic had a chance earlier in UE4s lifespan to fix this issue as they were fully aware of the issues in previous UE versions which was extremely similar just with the cylinder instead of the capsule. I understand why these classes are linked together but why they are core classes is what I never understood, why that functionality wasnt dropped further down into children so it was more readily overridable.
It might not be avoidable to create a new code path for the new system for backwards compatibility, issue is that creates something else to maintain which is why Im very cautious in the planning phase and it sounds like you took the time to outline a more modular system from the get go which does save alot of headaches like this in the future. There is always the possibility of not supporting those older code paths in newer engine versions and thats what I would personally prefer because I support any change which improves the engine 