Just a couple of ideas:
1. See if the dealer can add more of the semi-soft, black, rubber tape to tape the edges of the two small panels. If you look at some of the hardtops on dealership floors you will see a few inches (2-4 inches) of this material on some of the panels. This should be cheap and an inexpensive option the service department should consider trying for you.
If you think of the 'edges' of the Freedom Top panels, they are hard material (albeit lightweight) that fit to other hard surfaces. On many convertibles, there is a SOFT rubber groove at the top of windshields that seals with a HARD surface to create a seal. Think of ANY waterproof container like a Pelican case. The open area creates a seal with meeting a hard material to a soft material. Waterproof camera cases have a rubber gasket 'O' ring and usually require a coating of silicone to create a waterproof seal under water where water pressure adds more pressure. (Hard surface on case; soft surface rubber 0-ring; liquid waterproof gel). [Water pressure at 33 feet is equivilant to one level of barometric/atmospheric pressure; 66 feet is 2 bars; and so on.]
The silicone is probably not needed but the thin, 1 inch wide, black rubbery tape on the panels will probably improve the seal and solve the problem. Just don't go scuba diving with it! If you do, silicone won't help you.
Just kidding but hopefully this makes sense.
If you've ever done any simple plumbing and used teflon tape to water seal threaded pipes. Obviously teflon tape would not work as it would strip with removal of the panels but could be used elsewhere on the Jeep.
The rubber tape would probably need to be replaced every couple of years at very low cost.
2. Ask if the dealer can get you other panels for you hardtop. However I think that 1 above is the real fix. The new panel option may work if there is physical damage to the panels, enough to let water in. Path of least resistance rule of water does not require much damage to leak in.
Good luck! If the tape works, let us know and let's find out if we can buy a roll to keep in our Jeep repair kits.