You really don't need to have FastPasses booked for the people who are going to enter using the "rider swap". I can foresee a mess if you have 6 people book a FP and then the second 3 to enter don't actually use that FP, which would mean the people who entered second will not have used their required 'first 3" FastPasses before they can book 4th, 5th, etc FastPasses.
I admit I don't have any experience with it after the recent changes to rider swaps, but if it were me I would not book FPs for anyone who is expected to ride using a rider swap, book those 3 people something different.
But for the specific point of "which FP will the Disney system use when I scan if I have both a regular FP and a rider-swap FP", it's an interesting question that I have not seen an answer to.
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