Hi,
I also can't see how this function could ever have had any effect. So really, by changing the code so that it does have an effect, you are introducing a new feature. Looking through the mailing-list archives of the last 14 years, there are only four posts that mention the fluid_synth_set_gen2 function.
One person stumbled across it and wondered why it doesn't have an effect. The others came from the thread-safety changes when somebody found the function in the code and decided to make it part of the public API, because: "These functions were meant to be made public at some point, as the comment suggests at the top of fluid_synth.c".
So it seems to me like no user has ever requested or used that feature, at least not in the last 14 years. And it's not part of the SoundFont specs. I would vote to simply remove it.
Cheers,
Marcus