For Notification level settings, its a bug in the UI. The backend
isn't actually adding prowl to every notification type, the UI just
isn't being properly updated when you change between them, and could
be causing problems viewing the changes made in app a when returning
to it. To demonstrate, make the change to the very first note type in
app a, so that when you change back to it, that is the one which is
selected, the prowl setting should be there when returning to app a,
from app b.
This has already been fixed for 2.0.1 (or whatever the next release
winds up being called)