For the fly-by-wire system simulated in the Wilco Airbus Vol. 1 package, does it matter if the elevator/aileron axes are assigned via FSUIPC, or does it have to be set via FS9's internal assignments for the fly-by-wire to work properly?

Either way you cut it this add-on needs FSUIPC. You have to configure the throttle through FSUIPC so outside of your question you need FSUIPC. In short FSUIPC most likely has little to do with how this model handles Fly-By-Wire but just the same the add-on won't run correctly without FSUIPC. All this being said, make sure you have FSUIPC installed and everything should work as it should plain and simple (no need for rocket science here)...

most problems people have is because of mapping their throttle and yoke/joystick/sidestick through FSUIPC.i don't have my joystick nor throttle mapped and have no issues.the #1 thing necessary is the have a large enough 'null space' for the yoke/joystick/sidestick to 'center' and allow the fly-by-wire simulation work.#2 is to have full range of movement in the throttle axis, anything less and the throttle gauge will not now how to set the throttle range and gates.--