Also, being able to create jet fuel means less need for current fuel tank storage aboard a cv, which means extra room for other stuff like beer.
As hybrid cars become more popular and gasoline consumption drops, prices for jet fuel will skyrocket.
Another bad thing about the Navy being dependent on land based fuel reserve tanks is they are an easy target for future Mach 7+ cruise missile systems.
Also, consider survivability. If the stuff can be generated as needed, the storage capacity can be diminished as you note, and replacing a high-energy liquid fuel with something a tad less volatile, even if just empty volume, makes the ship more robust under attack.