Howdy all,
Alright, after hours of scouring the forum, I figured now was a good time to drop the question. First, this is a clean new install running v1.17 (1d8b790) - with URL Rewriting enabled and configured correctly.
First thing, the Mail Fetch user we have is working just fine with AAD. Can fetch/send emails with the same App registration in AAD without issue; was able to do the organizational consent, can renew its own token, it just works. Fancy.
For the authentication side, things get a little more interesting. From the same working instance (properly censored image below):

I checked Graph and AAD as well, the user attributes are correct as well. When a user or agent attempts to log in with OAuth2, the login as far as the App registration is concerned is successful, but then the session is dumped into the main domain helpdesk page with the user not signed in - this applies to the user login and the agent login window - either way the user is dumped back to the main page not signed in.
API permissions just in case I missed anything (all with admin consent granted):

Cheers in advance.