Yamaha (and the mfgs in general) are usually a little conservative on reserve fuel - if they say it is 1 gal, you'll usually get the low-fuel warning light with 1.2 gal left, or something like this. But 75% more than stated reserve would be unusual.
Of course, the calculated reserve is influenced by how full you get the tank. To make sure you don't pump fuel into the tank vent (which can screw up the charcoal canister on CA models), there is a standpipe in the filler and you're supposed to not fuel above this, although it is commonly done. It might be possible you're being overly conservative in how full you try and get the tank.
It's possible the float sender is miscalibrated. It appears to be a simple variable resistor, probably integrated into the fuel pump assembly. If this were the case, I would think this would also cause the fuel gage to be pessimistic, possibly not even registering a full tank after a fullup.
- Mark