The tune of a mass spectrometer adjusts mass accuracy, sensitivity, AND consistancy of ionization and fragmentation - thus the issue of matching peak ratio on BFB or some other tune standard.
If you are measuring the various gasses with mass spec, you want to adjust all of these factors (sensitivty, accuracy, consistant ionization) - even if the fragmentation of specific gasses is not interesting, to ensure that the ionization is consistant over time. Changes in fragmentation molecules will give rize to fariation in response. Even though you will run a check standard on a regular basis, and calibrate as needed, you want to maximize the stability of your measurement. And you have factors like the age of the filiment - which will change temperature over time as you try to maintain current - and energy distribution of emitted electrons - that work against this stability.
Unless you have a regulatory requirement that specifies what you need - you can optimize where it makes sense. But be sure that you cover consistancy of the ionization process along with sensitivity and mass accuracy. In some instruments, it is most convienit to use the built in tune (like on PFTBA) and keep the instrument optimized to that. And that may work well enough for you.