I would say that only applies if an MWBC is run. If it's two separate circuits, each with its own neutral, that's two 120V circuits, regardless of the voltage present between the ungrounded conductors of the two different circuits. So I'd say 2 single pole GFCIs without regard to which leg they are on is fine.
If someone says that no the ungrounded conductors need to be at 0V to each other, then after disagreeing I'd say that it would suffice to place the two single pole breakers appropriately at the time of installation; there's no need to worry about someone rearranging breakers in the future.
Lastly, if you do want to use a tandem because someone is worried about future breaker rearrangement, that obviously could be done by using two blank face GFCIs with a normal tandem.
Cheers, Wayne