Well, yes, in our environment the eap file is just a local thing and nothing to do with version control.
Say you have a branch in your repository "Project xy/Models". You check it out to a local folder, then create an eap file somewhere, add a version control ID pointing to your local working copy (where the xml files have been checked out), and get the root package from there. Check out one of the packages from EA's package control context menu, edit it, and check it in again from EA. Then EA will export to the xml file in the local working copy and check it in to version control.
The xml file is up to date then, of course, but you can see in the version control log who has checked it in.
As long as you have not checked in from EA, the changes you've made are only stored in the local eap file. So this private model strategy is allright if your usual scenario is to make small changes and check them in immediately. When you rather work on a model for days on end then maybe you'd better use a shared model on a network drive which is subject to backup every night.
There's a lot more to say about all this, and there have been many discussions in this forum. Maybe later today, when the Americans join us, or tonight, when Australia wakes up, we'll have some comments from the old hands.