This would be a local app-managed setting that adds a toggle to each community.
When enabled, this toggle allows all of the posts from that community to be combined with all other communities of identical name, from other instances under a common category name.
Because this is a per-community toggle, this lets you filter out communities of identical names from an instance you may be on, that you want to exclude from this category.
For example, enabling this setting on the identically named (and themed) communities of Fediverse@kbin.social and Fediverse@lemmy.world would combined all content from both communities together under a single category called Fediverse.
If there were another instance with a community of the same name but of a different topic, then leaving this toggle disabled for that community instance would exclude it from this category.
Categories can then be treated like communities in the subscribed community list, under a separate section just like how communities are split between All/Local.
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As an additional bonus, the app could ask the user if they would like to consolidate identically named communities. It would then provide a list of these identically named communities, with checkmarks beside them to quickly toggle this setting.
To reduce spam, if a user wanted to submit a post to this category, they would have to specifically select the community instance they wanted to post to.
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Lastly, if this idea of more app-managed consolidation is taken to the extreme, then perhaps allowing users to combine multiple accounts together across each instance could be possible. Where even if two instances defederate, if the user has an account on both instances, they can still view the content as normal. Perhaps this could be called global mode, where accounts only interact with the specific instance they exist on, but combines local feeds from each account/instance together.