I've found long flex runs can create substantial loss. I have worked for a couple companies and learned a few tricks about flex. One particular job, we had flex a couple feet out of the trunk, hard pipe about 10', and then flex to the boot. Flex, if not installed right and pulled tight, will create loss and higher statics. High statics, if extreme, can cause problems in the unit.
Go with the short flex runs at the boot as this will eliminate some noise. Use as much metal as you can.