I've seen some Lemmy apps/interfaces do that as well. So maybe it's not all that different?
I think what they're suggesting is that a post would have a merged view of all comments from all the different duplicate posts in all the different communities it's posted in.
To combine the comments would probably require a revision to the lemmy protocol, plus an even bigger one to the backend software to keep backwards compatibility
If it is possible to detect which posts are cross posts, it should be possible to create a client app that combines the threads. Maybe give you an option to chose which one to post your comment.
I was just thinking about a possible solution based on what we have. I agree it would be better if cross post comments were federated, but I guess there's different opinions on that (do the lemmy devs agree for example?).