It may be as simple as what tires they were putting on at the time they wrote the spec. Marketing might see the S as a selling point, but who want to drive the van over 100 anyway, if the governor would even let you. Most heavier duty tires are R, I think, except for a few brands and maybe more brands could be if they wanted to rate them there but do an R as a CYA to prevent bad things like somebody actually driving a van that fast.
I really don't know if the speed rating is mostly set by temperature gain or things like centrifugal force, but at least for me I haven't seen any need to worry about it. Our Michelin MS2s, which we just replaced with Agilis, didn't run hot at all once we changed the rear axle which was contributing a lot to the heat in the tires it appears.
The R rated MS tires handled and rode much better than the OEM Bridgstones at S, though.