Just checked the nips docs now and you are right. I would imagine the second format (nostrconnect://) is something the client needs to generate for users to copy and paste in their signer while the first format (bunker://) is purely generated by the signer and pasted on the client.

Ideally IMO, the nostrconnect format from a ux standpoint should be abstracted away into a button which signers can react to on mobile (deep-linking)