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.
I recall reading that the car JFK rode in was demolished before anyone could thoroughly look at it.