It has nothing to do with gains. It has to do with how the exu does fueling, and injector size as well.
On the gen 1, the ecu does not recognize and can't fuel according for boost. Because of that you need to mechanically fuel the engine. When I mean by that is an fmu is a 1:6 ratio regulator. For every one pound of boost, it increases fuel pressure 6psi. So on a stage 1 gen one hayabusa that means under boost with 8psi, the boosted fuel pressure should be around 90psi. By raising the pressure so high allow for the small stock injectors to flow enough for the turbo fueling, and also it a back door for getting around ecus that don't recognize boost.
The gen 2 ecu on the other hand can recognize and compensate for boost with injector pulse width. Don't need sky high fuel pressure to mechanically fuel with them.