I've registered a number of new/used vehicles and RV's in AZ. They base their registration fees off the "base" MSRP, before options are added. The AZ DMV does not use the data from your window sticker or any invoices you may have from the dealership to determine the base MSRP---they use their own internal, manufacturer supplied database.
Our '16 Ram Cummins had an MSRP of $54K (with $15k in options), but we only paid registration fees on the base MSRP of $39k (fees were ~$750 in 2016; currently ~$375). FWIW, someone who purchases the same year, make and model truck we purchased with the Hemi engine option (instead of the Cummins option) with an MSRP of approx. $44k, will pay the same registration fees as we did for our $54k truck. Reason being, both trucks have the same "base" MSRP (before options are added).