The datasheet is pretty clear that 5K pots are required. That much is true.
In practice, I doubt it's critical. There's one reason it might be, which is that the PedalSync chip's internal ADC likes to see a low impedance. If it's scanning the pots fast, there won't be much time for it to charge up the internal sample-and-hold capacitor, and a large pot value would mean that the capacitor would only charge slowly - potentially too slowly, meaning the value would be read incorrectly. Consequently, I might be tempted to try it with 10K, but I'd think twice about using 47K or 100K pots with it, unless they were buffered somehow.
I don't see any reason why the control pots should match the digipots. They're doing totally different things and they're not even related, except by software.
Your thinking about it looks spot on to me; the chip reads the 5K pot, sees it's at 50%, and then sets the appropriate digipot to 50% resistance. What actual value that is depends on which digipot chip you use. They all have exactly the same interface, so the PedalSync chip won't even know what value the digipot is. It doesn't need to. It just sets it to 10%, 50%, whatever.
Tom