if everything is fine in an application, you won't see issues with package annotations.
that users aren't used to it is an important part, because package annotations are quite hidden and usually unexpected.
esp. because they are quite unexpected, it can happen pretty easily e.g. during a refactoring/cleanup/... that the application behaves differently afterwards, but you don't recognize it immediately and later on most people just check the history of config file/s (and not the package-info).
@ "... the first version found ...":
yes - the behaviour you described is correct, but that's imo even worse. such issues are sometimes hard enough with classes (e.g. there are ee-servers which behave differently depending on the names of the archives -> something can work in application x and in application y there is the same setup but it fails due to different archive-names). since such issues are around for years a lot of people know about them, but imo issues caused by package annotations are harder to find, because package annotations are just unexpected and it's hard(er) to find the meta-data if it's e.g. a leftover in a different jar than the one you are looking at.
fyi: mark just told me that the cdi-eg dropped package annotations as well.
regards,
gerhard