I don't think that's possible, given the method how GEN handles the information and how it writes them into SH3.
The reall stopper here is SH3!
The GEN data has to be written on the layers of the save-game and the campaign layer...among others! Which is read on start.
There's no work-around there!
I really wish it would be possible! I'm using GEN since the beginning and it's a must have for solid SH3 Gaming!