Great stuff here, great detail. Real Product Manager thinking in play!
So with this point:
That’s almost like an feature that “watches” to see if something has been read. That would be very cool, too, but I assume a lot of work to build.
To this point:

Also, what scope do you see these messages coming from that would indicate to the author they had been read? In other words is it just for @mentions?
I do like it if you are able to “heart” ANY comment, and not just if you are @mentioned. This would work well with Watchers as you could get the comment in your Inbox as a Watcher, and then “heart” it, but not necessarily be @mentioned. So the commenter can just write an update generally about the watched entity, that may be of interest to all watchers. Otherwise, they have to artificially @mention each and every watcher - that’s awkward. This I think is a pretty standard way a lot of other apps approach this.
Thanks again!