Wire B is ground common to both outputs. Wire A looks like it's going to the Op-Amp on the audio output of Paula. So it probably by-passes the normal Amiga audio output filtering. Wire B is attached to a connector to allow the motherboard to be disconnected from the mods attached to the case, wire A will need to be unscrewed from the ground point to release the motherboard completely from the case mods.
Oooh. Great memory. I bet you're right. You can't bypass the audio filter in software on the A1000. (All other Amigas can software bypass, this is indicated by a dimmed power light when bypassing.) Those jacks are likely filter bypassed audio out.
