You can only federate via tor or i2p if both sides support those protocols, because for federation to work between two nodes both nodes need to be able to initiate connections to the other. That means one-way bridges like tor exit nodes are not sufficient.
I’d guess most Fediverse servers don’t support either of those protocols, so any new server trying to federate solely through them would have an extremely limited view of the Fediverse.
Though I suppose theoretically nothing is really preventing a motivated group of server admins from setting up a parallel “dark Fediverse” containing only onion sites.