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The value is in the granular way that you can connect communities. You’re totally right that there are a lot of cases where there are good reasons not to connect communities. That goes across instance borders (like you said, Beehaw and Hexbear would preferably not connect communities), but even for instances that are similar, not all communities need to be connected. In the current example of the Social Hub forum and the NodeBB development forum, only 2 communities (categories) are connected, and the rest is not.
Thank you for sharing the article! Please note that this is last’s weeks episode, the newest episode went out yesterday: https://fediversereport.com/last-week-in-fediverse-ep-70/