Because with Lemmy’s architecture darknet sites could not federate with clearnet sites as the end user’s browser fetches content directly from the federated instances.

Ehhh, that just seems like something someone hasn't fixed yet but easily could if built for that purpose. No one's taken a hammer to that nail yet.

A tunnel could exist on each server that relays to TOR and back to the instance, allowing it to federate with .onion instances under an alias or something. TOR is extremely flexible with tunneling and being really specific with what you let in and from where. I could see how it could be tailored to the purpose.