@p A "combo" instance is a clearnet service, and it federates with other clearnet instances as usual, by sending HTTPS requests. There's no associated onion/hidden service. However, when it sees .onion actor, it sends federation requests via locally running Tor proxy.
Tor instances still can talk back to it via exit nodes, even though there's no onion service.
So, if I understand correctly, such "combo" instance creates only one entry in FediList database and there shouldn't be any duplicates.