In reply to Justin Tadlock.

Managed to miss this reply somehow. So sorry for the delay. I found it while jamming away on the summary post today.

One of the things that is problematic — and this is coming from other theme devs, too — is that nav menus changed from just being data that we could manipulate to a very specific HTML structure with its own CSS and JS tied to it.

This has definitely come up a ton with the nav block implementation. I do think, in time, expanded options with theme.json will help fill these gaps but we have a ways to go there:
https://github.com/WordPress/gutenberg/issues/39052
https://github.com/WordPress/gutenberg/issues/34514
As you mention, it's also a mental switch to manipulate menus in this way!