Yes, they are a little too high, though probably not as much as some MTH and Atlas cars. My guess is they are about six scale inches too high. I suspect that if you lowered them just enough to match the car body up against the Kadee height gauge, you'd be close to the prototype height. And that's probably where you want to be as a practical matter in any event; any lower and your couplers will be off.
These TOFC cars don't ride as low as, for example, 89-foot tri-level autoracks. I think a partial reason for the extra ride height is to allow for the way Atlas mounts scale couplers on the two-rail versions (For those not familiar, the Atlas mounting plate is retained in the photo below). Remember also that the Atlas draft gear box top panel is a lot thicker than the Kadee draft gear box lid.
If you lower the body in accordance with the Kadee gauge, then you will have the problem of mounting couplers. If you keep Atlas two-rail mounting plate, your couplers would be too low (or at least out of the widely accepted scale standard). If you ditch that you'll have to drill into the body to mount scale couplers, and there's not much material in the deck to do that. I haven't tried it, but it seems to me that if I ever do lower these cars to that extent I likely would mark and drill and tap screw holes right through the body and the top deck (I would use 2mm screws). Then mount the couplers and cut the screws off flush with the deck. I doubt the fifth-wheel assembly will cover both scars in the deck, but a little putty, paint and weathering should do the job.
RM