Depends...what are the actual supply's voltages? 3-phase tends to be with the phases 120-degrees out of phase, so if the WH doesn't have any electronics in it, it would depend on what voltage you actually develop between the two phases you choose. A heating element just cares about the voltage between the two ends. If that's matched to the supply, doesn't matter.
In a really large situation, that unbalanced load on the supply transformer might be an issue.