Hmmm This is a really funny question that no one can really answer but I think I'm going to go with the gummi ship can sorta be summoned, why?
Well the same thing happens when we're at DC and we have to go find Merlin at Hollow Bastion, then Merlin seems to just teleport us back to DC without us having to fly back there...
Yet,
We are still able to catch the gummi ship back at DC, but hang on... Wasn't it left at HB, See?
We have the same problem,
So Naturally Im assuming the gummi ship can just follow them from world to world, or be summoned either way it works!