Providing AUCTeX as a package
As a package provider, you should make sure that your users will be served best according to their intentions, and keep in mind that a system might be used by more than one user, with different preferences.
There are people that prefer the built-in Emacs modes for editing TeX files, in particular plain TeX users. There are various ways to tell AUCTeX even after auto-activation that it should not get used, and they are described in the previous node.
So if you have users that don’t want to use the preinstalled AUCTeX, they can easily get rid of it. Installing AUCTeX as site-wide default is therefore a good choice.
You can install ELPA AUCTeX package under a directory listed in package-directory-list to have site-wide default.