If you use private torrents, chances are you want the swarms you participate in to be private, unless you're happy to announce your IP to RIAA. I do agree though that the current model in which cross-seeding between private swarms is an afterthought and a pain is not perfect. Clients should handle that automatically without having to resort to hardlinks and separate folders and heuristics to find matching torrents and partial matches and the rest of accidental complexity no one really wants.
There actually are BEPs to manage cross swarms sharing, but I don't know of clients that do handle that. BEPv2 should make this easier though, because each file has their own hashes on top of the top-level hash.
