Assign the route to the plane. Then open the route info (not the edit route), and see what it says. If it says 'limited to 24' there, then it might be a bug.
The warning boxes are just guidelines, and they say something like 'the actual limit will depend on the exact specs of the plane you use'. They don't work all that well for planes with lots of big variations, like the a300 family.
If the runway at both ends are big enough, and you've put a 5100 range setup on a 5000 NM route, every seat will be available. If you put in on a shorter range plane, then it might be limited to 24.
When planning ahead, it'd be good to be able to distinguish between them. I think I smell a feature request...