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.