NIP05 is just a simpler way to login, nip46 provider may issue you a nip05 under their domain and when you enter it for login all the data needed for connection is automatically fetched from a known location on the provider domain. So you don't need to generate a bunker URL on provider first, just enter your nip05 name.

The biggest concern for major native apps (and web DM apps) is DM decryption - apps store the full history of DMs in encrypted form on disk, and decrypt them all on startup, which might mean thousands of request to keys every time the app starts. There are many ways to solve this (decrypt on demand when user opens DMs, store DMs in plaintext, store them encrypted with local key, etc) but they all quite complex or require compromises, all while Nostr Connect is just not a priority. Especially when there are platform-specific faster solutions like Amber which Amethyst supports.