I think something like this is necessary at some point, since duplicate posts across duplicate communities is an inconvenience when compared to more centralized communities in Reddit. Some thoughts:
When you go to the comments, which instance's comments are we seeing? If we make a comment, which instance is our comment posted to? My idea would be to throw everyone's comments into a singular bucket as you said, but then you'll have to select which instance you're posting to when commenting. This does introduce an issue with moderation though, as different communities may have different rules. So there may need to be a moderation option on whether you'll allow post collation across other communities.
Aside from grouping duplicate posts like this, we could also group different communities. If we have a kbin.social/m/technology and lemmy.world/c/technology, we could just combine the posts from both communities into one group. This could be done automatically for communities with the same name, but a better option may be for moderators to add "sister communities" whose posts will appear in the magazine. That way, from the user's perspective, there is just one technology magazine that assembles content from multiple instances.