From the description in the c-store its built into the ability:
The ship comes with an Advanced Transwarp Drive Ability. Starfleet's "great experiment" of the 2280s, this ability allows the ship to instantly travel to the Alpha Centauri, Psi Velorum, Iota Pavonis, Beta Ursae, Alpha Trianguli or Eta Eridani Sector Blocks at no cost. The Advanced Transwarp Drive Ability also offers a constant passive bonus to Starship Energy Weapon Performance, Starship Shield Performance, Starship Engine Performance and Starship Auxiliary Performance which scales with level.
Just tested it, the bonus is not build in. I tested it with a Excelsior and it's T3 version - Advance Heavy Cruiser, also a Dreadnought. I remove all console/equipment on all 3 ship, and each i put on a white mark X and mark IV beam array. All 3 of them has the same dps which is at 283 (Mark IV) and 355 (Mark X). Also their energy level are the same as well (set to balance and result in 73/75/73/70 for every single one of them). According to "passive bonus" shown in the c-store tooltip, not only Excelsior should have higher weapon dps (due to +energy weapon), also the engine and aux. power level should be different too.
So question to cryptic, where is the console or it's bonus?
Just edit the original post, re-stating the problem, clearify a few things and try to keep the future replies productive. (I do appericate ppl stopping by trying to help, but there still half dozen replies are talking about totally different console/ship, so just try to make thing more clear)