Charlie is correct, the typical bus is also referred to as a bus bar as it is made up of a copper bar of significant cross section, that is protected by the fuse at the alternator output. As for the flap motor wires, they are sized and designed to limit the motor drive current and thus heat. If there is a short internal to the flap motor wiring, then there will likely be some internal wire melting requiring a new motor (these motors are typically too small and inexpensive to make a motor re-wind economic).
If your flap motor only draws 5 amps, you could probably use a 7.5 amp breaker, so long as the inrush current when the motor is starting isn't too much above 7.5 amps and is fairly short in duration. However, with such low currents, you are typically better off installing slightly larger wire to reduce voltage drop and then protect that larger wire with a larger 10 amp breaker.
Good questions though. Better to ask the questions so you understand than just follow the instructions without understanding why.