I set my tools to the spindle C/L (G54 X0) for all turning operations. Then I let Fusion generate the appropriate G code for threading. Then I run a part and check the result against whatever measuring device is appropriate for the job: Nut, mating part, thread gauge, or thread wires. If the fit is not correct, then I adjust the X cutter comp as needed to dial in the threads.
Bottom line is you need to dial the machine in as part of the setup procedure. This is true for all production turning.