I agree that is a logical initial step, but I wonder about ‘cross-posting’ actually catching on. Reddit often saw duplicated submissions across subreddits, but was able to collate them by the “other discussions” approach simply through url-matching. Relying on cross-posting also requires users to be members of disparate communities.
Maybe the act of defederation acts like a filter to a comment thread, or at least a “click-to-view”? Comments are there unless defederated or more simply blocked by the user. Much like users can block specific magazines, users, or instances, the same filters would apply to the comments.
Voting could also have multiple purposes: one to raise/lower comments/threads across platforms and perhaps a second to allow a user to sort by “votes from [instance]”. If you want to see what your preferred instance voted for toggle that (i.e. factor only votes from that instance) to get a new sort.