If I were to upgrade my HU to an after market GPS/audio system would the "Vehicle set up" menu be able to be changed/toggled off/on with the ScanGauge. I haven't seen any published codes for the Xgauge to change these settings. I'm assuming that being able to turn the backup beeper off and on, that the same would hold true for these other functions.
I think the short answer is you will no longer be able to change those settings. Make sure you have them where you want them before you take out the head unit
