I'm sure i am missing something, but why would someone extract a whole super at a time?
Couldn't you just take any number of frames from the super (that are full), brush all the bees off, and put them in a bee tight container?
Why WOULDN'T you want to extract the whole super at a time? For that matter ALL your supers at the same time. First off, there is the trouble to clean up afterwards. Second there is the waste of all the honey stuck to the equipment. The more you do at once the less waste of effort and the less waste of honey.
It just depends on the size of your operation, how much time you have, and how eager you are for that first honey of the season.
Many only extract once a year, which makes sense,do it once and you are done.
I will extract when I have at least 3 or 4 supers, but pull frames from multiple hives to get there. So I end up doing it a few times. Just depends on what works for you.
Is it less likely to granulate if it is left in the comb?
Out here, many beekeepers sell honey all summer long and rest during the winter. It would make sense to avoid granulation by extracting it as you needed it. I was thinking of doing that myself.
I would say the biggest reason would be clean up. It takes as long to clean up after 10 supers as 1 frame.