If you take the boat loop that runs from DTD to POFQ and then Port Orleans Riverside then yes the boat always stops at POFQ first.
On the boat dock from DTD there are different routes to Key West and Saratoga Springs, sort of like what you would find with the different bus routes at a Disney park. The BUS routes (not boat) at Saratoga Springs and Key West are kind of wonky with additional "internal" bus stops so the most efficient way to do the Boat to resort then Bus to park is via Port Orleans FRENCH Quarter.
That that being said, usually in the mid day hours the BUS goes from POFQ TO POR and does the internal bus route that POR has. So it's the time of day and the luck of the draw as to whether the BUS to the parks at POFQ goes right to the park or takes the detour and goes to POR as well.
Either way the detour to POR doesn't take that long and you will more than likely have first crack at a seat on the bus. I can't speak of the conniptions that you would encounter if you took the boat to say, Saratoga Springs, and then got on the bus. I only know the POFQ/POR bus conniptions!
Hope that helps!
~NM