To the best of my memory, we have guessed the vin numbers go with the cluster's.
If you check the map tables don't think you will find any difference.
SO the data not seen by TuneEcu or TubeBoy most likely is cluster info and MPG tables.
Many have loaded newer or older tunes than there bike would use and have not found any problems.
My custom tune was based on a much older tune, 3 button cluster. It's been installed in many 2 button cluster bikes and worked fine.