OP, the Axe III is a guitar processor. It is marketed as such, was designed as such, constructed as such... 48k for a guitar processor (given the audio range of guitar tones) is more than adequate. Changing the sample rate to 96k would necessarily cut the number of effects that could that could be used simultaneously — which is one of the main marketing points for this device.
It isn’t Fractals fault that you wish to use their device differently from its design / intent. Have you gone to the hardware store recently to complain that their hammers don’t cut wood?
Ok, maybe they can't increase it and it could be fine, but why they can't make 44100Hz available? it will also increase the number of effects that could be used simultaneously, it could be a real benefit.
Would you go to the hardware store to complain if their saw can cut titanium but not wood?
I think the answer is, yes.