Unfortunately, the overall answer to your question is yes and no.
I understand only too full well the problems you are facing. So I'll just give you the benefit (?) of my experiences.
Rather than having project teams start by creating their EA "project", I would like them to be able to start by reviewing the existing current state documentation that has been built up over time by past project teams. And at the end of each project, the future state system documentation that the team created would be stored centrally as the new current state. In effect it is no longer "project documentation", it is now "system documentation".
I consider the model delivered at implementation to be part of the configurable system, that is, the model, the implemented code version, the source code and the system configuration data should all be stored as a single release. All of these should be locked from change.
Everytime a "point change" is made to one of these, say for a patch or a system config data change, the reference data (the model) as well as the operational data should be adjusted. A modern VCS will provide the necessary lock control via check in check out but still wont ensure that maitenance programmers etc will update the model. Cie la vie.
When a new release of a system is undertaken as a project, the entire suite should be
copied out and managed by the project team until implementation, whereupon it should be checked in
in toto as a new release after archiving the retired version.
That is, the project will need to use its' own VCS during the project.
This to my way of thinking is better than trying to use the model as a separate entity to the implemented part of the system.
Now EA, viewed from this point is an excellent tool. It has fairly sophisticated VCS integration capability and functionality.
However, I have also found many instances of projects that involve the models from more than one system (or component). And it is here that EA (and in fact all the other products I have used) falls down. You cannot easily integrate external "reference" models from other systems. This usually means that each team tends to build up a different view and set of documentation for these, and over time confusion and error creep in.
But finally, having used about a dozen tools over the last decade I have to say that EA is the best by a country mile.
hth
Bruce