Dave,
I think you are going to have to version - in some fashion - the diagrams. My take on what you are doing versus how EA will react is that you are going to end up with something along the lines of a set of diagrams for each time period. Or perhaps somewhat different depending on how or whether these periods are syncronized, but that's not the point here.
Still, you are proably in good shape, particularly considering your last point about what you are looking for.
If you do need to version diagrams, remember that the "version" is what you make of it. It is a character field (length 50 in the Jet schema) so you can make these human readable, or key them to time periods, or whatever. This is particularly easy to manage if you use an add-in to do the leg work.
Consider collecting diagrams into sets based on the common revision points or periods, then putting them into packages to keep them grouped. Name the packages appropriately, and place them at the right point in your project tree. You can even move them (the packages) about over time to provide archiving or historical perspective that can be easily grasped by viewers. [You will probably want to uncheck Highlight Foreign Objects in diagram properties. You may want to consider using Diagram Notes in some standard manner for these, depending on corporate usage guidelines or preferences.]
A bit of a long shot here, but I wonder if you could use something along the lines of a transform script to do the heavy lifting. Don't spend too much time on this, since I think it implies changing the actual background structure of your model, and that sounds like the wrong approach. You definitely could write an add-in for this kind of diagram evolution though, and it could definitely help in the details of placement and versioning, as well as going through an inventory of diagrams to ensure completeness and consistency.
Let me know if this helps. I'm getting more interested in this idea.
David