The only thing that should happen is both functions get turned on and off at the same time. What might happen is if you don't know that CF is attached to the same switch as the GPS, you may get awfully confused about why the MK doesn't respond correctly to the sticks if you try to move it in any direction while the GPS is engaged.
As to how it could happen, well that has little to do with the TX for the most part, the poti assignments are done in MKtool and that would be the only place I can think of where the poti for a single switch/channel could be assigned to two different functions. I know of no way to assign a TX switch to two different channels at the same time which is what it would take to have different poti assignments in MKtool but operating from the same switch in the TX. Only other possibility is the TX is mightily fubar'd for something like that to happen.
Ken