This is for the haters...
Did you check the Necron FAQ on GW's website?
You do realize that this question was already answered, with the same exact source, a while ago right?This is actually covered in the 5th Ed errata:
Its in the same answer as 'Can the Monolith fire the particle whip and flux arc on the same turn.'
The particle whip is measured from any of the flux arc guns.
Fluff reasoning would be that although the crystal generates the power for the PW it is still shot through the flux guns. This would also explains why it can't shoot both, the crystal is either generating a medium amount of energy and projecting it out through every gun, or send all of it's energy through one.
You can find the errata here;