I think you're getting confused with things that happen for simulator purposes versus things that happen in real life. A lot of the services that happen within GSX would happen with or without the pilots on board. For instance, the pilots wouldn't be calling for catering, which is something you as the user would have to do in GSX. As for the refueling, from various videos I've seen, the pilots would generally finalize the amount of fuel they need and order the fuel before they board the flight. Refueling takes the longest time, especially for a long-haul flight. I can't find it now, and I don't remember where I read it, but many years ago, I vaguely remember reading that when Qantas flew their 747s in to LAX, with the exception of the flight that continued on to JFK, the plane would sit on the ground for a good part of the day before making the return trip to Australia. What they would do in the interest of saving time was pre-fuel the planes to a certain amount, then when the flight was getting ready to depart, they would finalize the amount of fuel they needed and then load the remainder of the required fuel. The pilots wouldn't be on board the airplane at that point in time.
On the actual airplane, you wouldn't input the amount of fuel you need in the FMC or EFB in order to load the fuel on the airplane, that's just something that's done in the simulator to make it easier to load the fuel without having to go into a separate window to do so. On the actual airplane, the fuelers would enter it in on the refueling panel located at the refueling point on the wing. Basically, there's a lot of functions that the pilots wouldn't handle in real life, but that you would have to in the simulator since there's nobody else to do it. Hope this all made sense.
