Right now those two races have most of the same bikes in them and the 500 Supersport champion rode a 250. That would cut into the number of entries in the 500 race significantly (there were only one or two bikes that ran in the 500 class all year that weren't eligible for the 250 class as well) and make the 500 class pretty skimpy until it catches on well.
We might consider combining them, though, as the rules currently being considered make the 250s ineligible for 500 competition. The current consideration is to make the 500 class legal for ONLY Ninja 300, R3, CBR250RR, RC390, and CBR500 with the likely addition of the GSXR250RR when it comes out in 2018. There is no verbiage in there to allow the "inferior" older 250s to compete in the class....though I suspect it will be added after this is read by a few people.
As with 250 SS NO INTERNAL ENGINE MODS ARE ALLOWED IN ANY SUPERSPORT CLASS (250 or 500)....though for 2017 we will allow the use of race gas in lieu of pump gas.