Actually if they set that in, you'd be gimping yourself in the DOff department, since Diplomacy and Marauding don't cross over.
Also, it would mean you could run up fed until LCdr, get the Point defense console, switch sides, get the neural-warhead for free, switch sides again, rinse, repeat, which would unbalance the game in the Romulan favor way too much.
They've already said it's not going to happen in podcasts.
Afterall, what happens if you're flying a federation ship.. and were able to defect over to Klingon? Would you ship suddenly go poof? Q suddenly decides to send your Federation bridge officers away on a permanent holiday? etc.
I am actually rather curious as to what happens if a science officer manages to level up to the point of being able to use photonic fleet without picking an allegiance.
You know, now I'm curious too. If I'm going to guess (and its a guess) it seems Romulan defaults to Federation. I say this because having tested a Klinkrom, all the text bugs, the DOff bugs, and the like seem to be bugged because they are defaulting to Federation.
So that said, my guess is you'll call in Federation ships.