Heh, right you are. 
It’s the same comic book store, and they got the same people to make the sign for Brodie’s store who made it for their real-life store.
Also, Montfort, Joey Lauren Adams and Kevin Smith are actually still pretty good friends. She was even going to do the commentary for the Chasing Amy Criterion disc shortly after they broke up, but there was a scheduling problem (though Kevin speaks very highly of her on that track). The break-up wasn’t the reason for the her lack of parts in Kevin’s movies.
The part of Bethany in Dogma was originally written for Joey, but the studio meddled with that (plus she ended up being busy at the time of shooting, anyway). They said that they needed a bigger star to play the part (also the reason why Baby Dave wasn’t the cinematographer on Dogma).
Kevin’s next movie is a drama/comedy, along the lines of Chasing Amy, starring Ben Affleck. Kevin is very much hoping to get Joey and Jason Lee to star in it, as well.