I'm a dumb a$$
The shift points are controlled by two things, mph and RPM, since your speedo is reading lower it may not make the speed needed to shift but thats pretty unlikely (but its possible, setting shift points is kind of a trial/error thing usually and I have seen diffierent tire sizes change WOT shift points) since most people keep the mph for the shift points fairly low and control upshifts with the rpm..
The speedo calibration being that little off has nothing to do with your idle.

