Couple of things, and I should add that I have no GM authority.

-You can pump alternative energy into a Transformer [i]all[/i] you want but it will have no effect. The only energy to work on a Transformer is Energon. 
-The space bridges in Transformers basically requires two hyperspace gates. Ships (As far as I've ever read and known) do not have their own FTL capabilities. However as far as I am aware this has never been proven or dis proven in the animated series or the movies.
-Just to make you aware (even if you change to Autobots and want an alliance) that you will never get [i]close[/i] to my ship once we find out you're giant walking talking robots. Especially being a Cylon War Era Battlestar. IT is also a problem for you considering I have high yield kinetic cannons a lot more powerful than a SABOT round. Tear you to shreds <3
-Not to mention you wouldn't be able to fly close enough to board me FLAKBARRIEERRRRR

IMO if you are determined to play Transformers, especially the badguys it would be better to have a small team who can just take on the look of ships and fly around. Lot easier to hide that way.

Just my input. Autobots might be able to find a way to get me to at least not shoot them(after the first encounter) though I don't know about any other times.