This shouldn't be a problem. There is an instrument mode in the Pitch Factor and guitar mode is set to standard guitar tuning, but it will also recognize lower notes, so this should be fine. If you do run into problems you can set it to synth which should give you a wide range of tracking options.
If non 440 tuning is what you're looking for, you can also do this by changing the tuning preferences in the system menu. This will also change the tuning in the tuner, so you can make sure that you are in tune with the PitchFactor.