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you're assuming the FPR works by measuring pressure in the rail, while it doesn't. The stock FPR and most AFPRs are simply throttling devices that create a pressure differential by blocking a certain amount of flow. Regardless of how much pressure is in the line, the FPR will open and close its "valve" based on the manifold vacuum/ pressure. It isn't closed untill it reaches a certain psi. Therefore, since you have a restriction at the 2nd FPR, pressure is higher after the 1st FPR than it should be, so the pressure differential that the 1st FPR is set to create causes higher pressure in the rail. This train of thought works for both setups, having the higher pressure FPR as 1st or 2nd.
I'm fairly sure that's how it goes.
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