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As far as i see they both require a 2.5 V and a 1.2 V rail.So the only difference would be how much current each rail needs.(please someone verify that fact)
AFAIK: Correct.
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If the power supply of the Spartan 6 series and the Cyclone IV turn out to be really interchangeable i see no reason not to try a prototype for both based on the same board.
Same BOM, but different boards: the pinout is different. Though much of the development work is identical, redrawing the layout for the other chip is a lot of work.