I'm not sure I understand? Your OP was stating that increasing duct size reduced the flow,but it appears this is not the case if we use the velocity readings.
Yes, you want the higher duct velocity. A velocity of 2500 FPM is too low for wood dust, IME.
As far as importance, flow comes first to get the dust in the hood. The duct is sized for flow to maintain velocity.
Mike
Edit, I would agree based on your readings that the 5" is preferred over the 6" because the velocity is higher, not because of your flow readings. Your fan would need to do 700-800 CFM in the 6" to keep the velocity high enough.