Why can’t some of these masked rioters be prosecuted on Federal rioting charges?
IMO they could be, but the police deliberately were not stopping or identifying them so no prosecution is possible until the police and the University get their attitude adjusted. They are effectively encouraging the riots and beginning the steps toward an actual insurrection.
Because it was not on federal property. Jurisdiction falls to the state and locals. However the feds could bring civil rights violations against the rioters or the city and university.