OP is asking about short and long bed versions on a Crew Cab. Yes, an extended cab with long bed and crew cab with short bed are the same wheelbase, but that's not what they are referring too.
A crew cab AND a long bed are pretty rare, so that's why the dealer is telling you they are scarce. So you want 5 seats and a long bed? The extended cab still has two jump seats in the back, if you can deal with that then finding an extended cab with long bed will be easier. As to ride quality, I'm sure there's a difference, but I am willing to bet it will be negligible. The amount of weight on the bed would make more of a difference than its length I think. Looking for 2nd or 3rd gen?
I needed to look up the options myself, but here's a quick illustration of the 3 possible combinations, essentially the same for the 3rd gens.
EDIT: Looked up the 3rd gen and made an illustration for that one as well next to a 2nd gen.
EDIT again: Added bed lengths, and options.
