Two posts, two different instances, two different sets of comments. Ok, there are pros and cons:
Segmenting the conversation means that different opinions and perspectives have a bigger opportunity to rise to the top in each discussion. That’s good.
There is also a risk of too few different viewpoints being present in one instance or another, making the possibility of an echo chamber forming higher. That’s bad.
I’m not suggesting that there’s a single perfect way to handle it, nothing is that black and white, but maybe there is a chance to do better. Perhaps crossposted content could contain a second link underneath between the body of the post and the comments section that could inform users that an identical post existed on another instance. Perhaps the comment sections could be merged but the user could choose to filter by instance if they wanted to.
I'm not sure about that. For actual cross posts, where the server is aware of the posts that are connected, it'd just be a matter of fetching all the sets of comments rather than just the one.
For when no one has actually cross posted but just posted the same link to a different community, that gets slightly trickier.
Any sort of solution though would require some service, whether on the instances or a separate bot, to scan for identical URLs and make connections for the frontend or client to then use. In such a case, the backend would need some idea or structure for a post hoc cross post, which would identify separate posts as being related in a way separate but similar to the cross-posted information.