If you really look at the photo of JFK and Connally siting in the car, you might notice that the angle of the pic has the front end of the car at a downward slope. Righting the slope might just place JFK and Connally on an even plane. What do ya think?
or maybe the picture taker was holding the camera at a funny angle....
Even if you rotate the photo so that the limo is on a straight line, you will see that Connally, a larger man than JFK, is sitting in a lower seat.
Or google JFK limousine - there are lots of photos of the limousine on the web, you will see that the middle seats in this model appear to be foldover jump seats that sit much lower than the single bench seat in the back.