it's not arbitrary
gnd/neut is 0 V or the reference
I agree it is not an arbitrary choice, as many objects in the vicinity of electrical installations are earthed, and so when one circuit conductor is earthed, it may be convenient to choose that conductor as the 0V reference. But that is still a choice.
Here's a thought experiment: say I have a bunch of equipment that operates at 40 VAC. I choose to use a 120V : 120V isolation transformer where the secondary is tapped twice, producing three equal segments and 4 circuit conductors. Call the circuit conductors A-D in order. The voltage A-B, B-C, or C-D is 40V; the voltage A-C or B-D is 80V; and the voltage A-D is 120V.
Now NEC 250.20(B) requires me to ground one of the circuit conductors, but 250.26 doesn't specify which conductor to ground. I can choose to ground conductor A, take it as 0V, and then the conductor voltages are (0V, 40V, 80V, 120V). I think we can agree that in this case legs B, C, and D are all in phase.
Or I can chose to ground conductor C and take it as 0V. Then the conductor voltages are (-80V, -40V, 0V, 40V). Are legs B and D now out of phase simply because I've moved both the earthing point and the 0V reference? No, they are still in phase, their voltage ratio has simply changed from 3/2 to -1.
Cheers, Wayne