I suppose an issue would be interfacing between clearnet and darknet based hosts, I'd assume there's need to be instances that act as a bridge, and for the sake of anti-spam would be better to use an allow list than open federation ( we should all move towards allowlists anyway and formal processes for small instances to be put on allow lists because blocking individual instances is simply not realistic moving forward ) 

 @26318dfd clearnet and darknet hosts can interact without a bridge. The clearnet host should be configured to send requests to .onion/.i2p hosts via Tor/I2P proxy, and darknet hosts usually don't need to do anything special, they just connect via exit nodes.

For example my instance can talk to both onion and i2p hosts.