WOW!
Unless the vehicle was "hit hard" on the sides, and incorrectly repaired, I consider this a major factory defect!
The problem is that, because of the mileage, Chrysler isn't going to see it that way.
Silicone sealer will stop the leak for now, but IMHO the only correct repair, would be to have them welded. Unless this is done, I'd be very concerned about the cracks "growing".
Welding the cracks would almost certainly involve removing the headliner, and all the trim and roof rack in the vicinity. Of course, after that, there would be "finish work" including painting, and reassembly.