For me, (creating a new user on MacOS and logging in and using only that new user, starting from scratch with Apple Mail, creating all the needed accounts), has been working well for just a little over 4 weeks now. So, not long enough to know that this problem is fixed.
I do see other "issues" (BUGS!) in Mail that make me think of memory leaks and the like (a.k.a. BitRot). There is still the issue of displaying Exchange mail messages with the same subject only displaying the content of the first message in the sequence. Also, sometimes, when reading a Message in Apple Mail, while Outlook properly shows a message as having been read, the Apple Mail client does not change from Bold to non-Bold and does not clear the little circle so, in Apple Mail, it still looks like it is unread...
So, which was asked, as I read an email in Apple Mail, within a few seconds, the email entry in Outlook changes from unread to read. When I delete a message or move it to another folder (on my system), the message disappears from the list on Outlook. Outlook even properly reflects the flagging (though only represents a single colorless flag regardless of the message's flag color in Apple Mail).
The whole experience is still frustrating as ****. I'm told by Apple support that if something works with a new account, it is not an Apple problem so they wash their hands of any further troubleshooting. On that score, the "Console" program, where I'm ostensibly able to look at logs, is REALLY FRUSTRATING.
Ok. Anyways, things still seem stable with Apple Mail and exchange.