In that case there should be corresponding cherry picks on multiple branches in the repository, and it'd then be those that should be linked together.
Yes, but the commit filter doesn't know which those other commits are. I guess it could try to build up some kind of database, so that if it sees the same commit being merged a second time it would look that up in the database to find the sha of the result of the previous cherry-pick. But it's non-trivial, so I won't implement it unless it's actually decided that it's a good idea...