Yes the e tags in 30040 events reference 30041. The reference format is kind+pubkey+d-tag, IIRC. So the e tag references should include a d tag that shows up in some 30041 event.
e tags in 30040 can reference any event kind, includind 01 or other 30040. We just defined 30041 as the default kind.
Ope I hadn't thought about that yet! We'll need to add some extra rules for rendering non-30041 events in our viewer.