For example, one can imagine a mathematics & physics oriented instance where LaTeX is available, or a chess-only instance where you’d have things like chessboard.js to allow members to post chess diagrams etc…

An interesting idea. But the problem with that is that the custom rendered content would not federate properly, so such communities would only really be usable to those on that instance, which destroys the whole point of being federated in the first place. Unless they were able to implement some sort of 'graceful degradation' so the content was enhanced on the main instance, but still serviceable on other instances.