People have been successful in manipulating the values of the boost controller code and getting more power (in a realistic manner).
You have to remember, if you want to properly swap turbo's, the controller code has to match the turbo for it to be a stable swap, you can get weird power maps if you mix controllers and turbo codes.
Go to this thread for guidance:
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But you're right, hopefully GT6 we may get more options than just Stage 1/2/3. Boost controllers are an essential part of tuning a turbo car, they should be in the game!