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Magic Kingdom and Epcot will separate the two resorts quite often at the peak closing-time rush.
I've never seen the Studios do it, but on mega-peak days it wouldn't surprise me.
Animal Kingdom I doubt would ever separate the two, same with the Downtown Disney route.
The buses that pick up guests at French Quarter almost always also stop at Riverside before going to the parks so they don't go to the parks with a partially filled bus. So they stop at Riverside also.
Someone who stays at French Quarter will therefore seem to see that the buses are always shared. What the guests getting on at French Quarter don't see, however, is that Riverside also has its own buses. The ones coming from French Quarter are extra.
At the parks there are separate bus stops for Riverside and for French Quarter, except at DHS where there share a bus stop. It looks like WDW ran out of space for bus stops at the Studios.
During the middle of the day when there are few riders the buses may serve both resorts.
They do share but its not bad at all. They are RIGHT next door to each other and the pickups arn't very large. When I went in December last year we picked up about 10 or so from the main pickup and the other stops just a family or 2