Something called external stores drag + weight, plus percentage additional weight of weapons and stores and BPR.
It's common sense. If the F-35 and Rafale need to get to a point in the sky that's about 200-300Km away as quickly as possible, then the Rafale can supercruise its way far more quickly than the F-35 can subsonic. Furthermore, at dash speeds or close to it, the F-35's not going to get more than 100Km range, so it can't compete anyway. So the Rafale will still have far more fuel for a fight in the end. All of this is elementary and doesn't require explanation.
You consider fuel fraction from before the aircraft has even taken off. But the closer and closer the jets get to the enemy, the F-35's fuel fraction is going to drop considerably faster than the Rafale's. This is what pilots concern themselves with, not the fuel on the ground that you have considered.
The only advatange the F-35 has over the Rafale in terms of performance is its ability to be scrambled faster with its one engine. It's a pretty big advantage for the Swiss since their main mission is QRA.