Is the primary purpose of this mod to have a better generator or lose weight from the flywheel? If it's just a weight thing wouldn't it be cheaper to get the stock flywheel lightened, or is the GSXR one so much lighter that would never be able to get enough material skimmed off the Honda one?

... I run total loss on my race bike, I was thinking of going with the gsxr mod but could I just run without a flywheel ... which is the best option ?

I would say for short circuit racing total loss is better but you may have to charge it during the day
I have run total loss on race and trackdays and always put bike on an optimate after each session,
I just think that with a lightweight alternator i wouldnt have to