They move with each other.... reduce your injector flow rate in your tune and you'll have to reduce your MAF readings to get correct fueling. Some of the Gen4 PCMs have a hard coded limit of 63.5lbs for the injector flow rate table, so if you fit injectors larger then that in those vehicles, then you have to 'scale' the tune.... which is putting in a flow rate lower than the real flow rate and then adjusting the airflow tables to get correct fueling. You also have to adjust spark tables when you scale the tune, because the PCM is seeing a different cylinder airmass.

You can use any number for the injector flow rate and then tune the MAF and VE to that injector flow rate... it just becomes a 'scaled tune'. When the tune is scaled, it does create other problems with the PCMs internal calculations, mostly relating to torque calculations.... so it's always better to use the correct injector flow rate when possible.