The engine computer does not know your actual ground speed. Speed readings are based off of wheel speed sensors which have a higher frequency the faster you go, so I agree that the bigger tire turns slower so will give and artificial speed reading vs actual speed. But if you are serious about testing top speed you need better equipment than the factory speed-0. seriously, unlimited a Raptor could probably push 150 top speed. You are limited (unless tuned). Older Superduty are limited to 95, not sure about 2011 and newer they may be 105. I would love to see a data long of wheel speed. I bet a dollar the "bump" is 105-106 according to the vehicle network. The speed-o is driven by this signal but the stepper motor and even the printing of the numbers on the instrument cluster has a tolerance you are well with in that tolerance.
It isn't like you are claiming 135 mph and I am calling you a liar, I am stating that 109 shown on speed-0 is with in tolerance of the 105 factory limiter. I also agree bigger tires would slow the speed signal down which in turn would give a little more real speed.
Factory tires are speed rated to 118, Ford is not in business for law suits and has no intention of pushing the limits. Ram did 112 on the TRX just to beat the Raptor ( I assume the Raptor R will be higher)