It's definitely bizarre the wire colors change. I hadn't even realized this myself (have some changes planned for my 2018, but haven't had the time to sit down and really look at things closely). I don't think they would do this to make upgrading the audio system difficult, but I would be curious as to why this is the case. Also in your model of vehicle I believe the front mids and tweeters are connected in parallel, so this likely makes it further difficult to tell which set actually makes it's way back to the amp.
A continuity test is done by setting your multi-meter to continuity mode as indicated by the schematic image of a diode:
. If you then plug the leads into their normal voltage measuring slots and touch them together the multi-meter should read "0". If your multi-meter has a beeper/buzzer that should also sound when you touch the end of the leads together (sound may need to be manually turned on). The test is to determine if the wire goes directly from one point to another, or if there are other electrical components/shorts in the way. It's similar to testing resistance but in this case we don't care about the resistance measure, we only just want to know if the wire is continuously connected.
The way I would do this is to take the speaker out of the door & disconnect it (since you're doing this anyways), then connect one end of the multi-meter to each one of the speaker wires at time in the door, and probe each output wire at the connector for the amp. Do this for both wires that connect to the speaker in the door and you'll know for sure which wire is which, plus you'll also have the benefit of knowing you'll have the correct speaker polarity for your aftermarket speakers when you go to hook those up.
Regarding the amp inputs/outputs and their respective harnesses, these amps are pretty universal. The basic shell design (probably PCB as well) is extremely similar-if not the same, for the entire Mazda6 generations of vehicles, so it would be far easier/cheaper for Bose to just reroute output channels to other available pins rather than go through the trouble of redesigning a new shell and changing the plugs just to compensate for a couple extra speakers.
EDIT: So I had changed out my 3x front channel speakers last week and visually at least it appears the wire colors going to those speakers correspond correctly to the wire colors at the amp harness. I can't confirm for sure without a multi-meter this is the case, but from the pin locations on the green harness and how all 3x wire pairs are exactly next to each other horizontally, I doubt there's any change in wire color from the speakers to the amp for me. I'm not sure why things are different for you.