Pick ups can have diffrent out put depending on the windings and magnet strength. The stronger the magnets, or more wire density will increase the out put, or "hotter" the pick up will be. Basically the metal string vibrating through the magnetic field crates a charge thats then translated into sound by the amplifier.
I'm not sure if acoustic pick ups are the same, since I've noticed some are not placed directly under the strings so I suspect they may work more like a microphone, which picks up sound by a mebrane vibrating a coil of wire around a magnetic pole. Esentially the same end result just a diffrent means. But would mean the pick up may be more dependant on the guitars resonance and not as responsive to the strings actual movement.
Sorry I'm not an expert, but hope thats useful.
As for the pedal, it most probably will sound diffrent with an electric guitar, just because acoustics have their own distinct sound, their bodies are designed to amplify the sound of the string vibrations. Especially if the pick up is what I suspect, a microphone type. Where as electrics depend on almost completely on the pick up to amplify the sound of the vibrating strings.
I don't know about the USB thing you mentioned. Have never tried to connect my guitar to my computer.