Not only will the pop-ups possibly cause alarm amongst many users, but as has been said already, if they are nothing that a user can do anything about and are only informational, then they will be seen as a nuisance.
It seems that Alwil team is already thinking how to deal with the notification in "another thread".
What I really want to know is this...does the self-defense module need to be disabled while installing new programs? Can it interfere with installations?
As David said, you don't need to do so. As you can see it from the notifications, all the files and registries are related with Avast! only. I thought XPSP3's dynamic overhaul could require such changes but, according to alanrf's comment above, it's more of the problem of XPSP3 setup. The same thing is said about the AOL app: They shouldn't require such changes if they were well written.
The issue seems to be about communication. Self-defense module is properly working except that it scares users with DOS window like black screen in a rather non-human-friendly manner.

I, myself, has no talent of programming and rely heavily on "documentations" when it comes to computers.