They will work together. You have nsec.app on your phone and an extension on your laptop’s browser. The extension generates a key for the communication with the bunker, and you approve it once on your phone.

The websites that you browse don’t need to even know that you are using a bunker. They will simply use NIP07. 

 I understand, but our primary use case for nsec.app is to onboard people on the web (on nostr sites) into a web-based key storage, without asking for extension install, so we're focusing on that part. If someone adds nip46 to extension I'm totally fine with that, it's just not our focus.