That would still create a fragmented comment situation. Ideally, the server should be aware of “sister communities”, so it could merge the comment threads, or at least tell the client to do so. But that has all kinds of moderation implications, as noted elsewhere.
In the end you’re either doing federation on community level (which would require another level of federation administration - you can’t just merge like-named communities from Any instance), or you’d have to convince 1 community to go read only and refer to the “defacto” community.
The first one has a lot of technical hurdles (servers and clients would have to adapt, and then community admins would be responsible for deciding who to federate their communities with). The second depends on mods giving up their community, which is unlikely and undesirable in case of defederation. Or option 3: keep the status quo, of course.