The archive ability which is available in all versions of the airport utility except the early v6, where it was dropped for a time, is designed to do a full backup of the TC. It cannot do what you want.
It cannot incrementally backup. Each time you press archive it will do the whole disk.
you cannot select folders to be included or excluded. The airport utility is an extremely limited functionality tool.
I am trying to avoid dragging files directly through my Mac. I want specific files (instead of entire drive) to go from the TC > External USB
A TC is a dumb as a board hard disk in a router. It has no controls like a real NAS would have, like backup with a auto controls and ability to deselect items or do incrementals.
So you have no choice whatsoever on a TC except for the files to be processed via the Mac.
Carbon Copy Cloner is one backup utility that can do the job. But it will be extremely slow if the material it is backing up has to be copied to the USB on the TC. Still if your changes are not great, it can be set to automatically do incremental backups on a daily basis.
It is much faster btw to have the USB plugged into the computer, so files do not have to be transferred back to the USB.. and this is x10 if you are using wireless.