How can a player without Entrenchment have a star base in the game if they don't have a game that is star base aware!!!!
Separate MP exe that can access all installed assets and toggle them on and off at will.
This means different values assigned to units (e.g. carrier build rates) and any number of things that would cause a desync.
Then create a single set of values for MP. It's just a balancing issue, and those will come up anyways.
How is a vanilla Sins player supposed to kill a fully upgraded starbase without any of the anti-SB units that come with Entrenchment?
I agree that some balance issues would come up, no argument there. But personally I think it'd be better to have the playerbase united with such a small community - Sins is not and will never be a perfectly balanced competitive MP game that would draw in a large community. Around 100 players at primetimes is barely enough, let alone divided by X.
Also, the game lobby could show which players have access to which expansions, allowing for balancing team assets. Add the ability for the host to toggle which expansions will be used in a game, and you can negotiate with other players what bits you want to use.
Finally, you can always assign different roles to people in team games. The vanilla player could go econ and feed the others, or just do fleet operations, while expansion players could make starbases and anti-SB units, for example. It can be made just a question of teamwork, something that this game doesn't really promote very well.