Because the fia want to encourage their own series to be used as the main feeder and drive backing through this.
Pretty sure the F1/FIA would be delighted if more IndyCar drivers came to F1. Anything to help build that American audience. Do you remember the fuss around Juan Pablo Montoya joining F1? Huge interest.
That aside: using the Super License system in the way you suggest would be a real twisting of its original purpose, quite inappropriate I would say. And, if it is true that is what they're doing then I hope Herta gets his exception because that's the purest steaming male cow droppings.