I have 4 seperate tanks on my 28' CC. 2 75's and 2 50's.
Advantages are they're saddle mounted, not sitting in the bilge. Less likelihood of them sitting in a constant salt water bath.
We used to go the Bahamas a lot and I always burned off the 50's first then refilled them. That way if we did get a batch of bad gas (never actually happened) we could swap out the fuel water seperators, open the main tanks and still have a safe 250 mile range. Enough to get back to the States.
I don't know of any boatbuilder that builds both ways. That would be a bit too expensive.
As far as filling up problems, I pull right in the middle of two rows of pumps and fill both sides at the same time. The owner of the gas station I frequent has no problem with that. I buy a little more than the average car that pulls in.