I'm optimistic that you'll be okay, but I'll keep my fingers crossed on your behalf. Even though I ended up replacing my entire braking system, I don't think it was necessary. That is, I don't think there's any reason to worry about the brake system on the Continuum Onyx, specifically.

If I could do this over again I would have replaced just the rotors and pads, simultaneously, once the the squealing got bad the first time and coupled that with a lever bleed. I suspect a lever bleed is all you need to reduce the pull before your left-hand brake engages. It's quite easy even the first time although I was nervous to do it. The only trick is getting a kit with a funnel that will properly thread into your lever. Once you have that, however, it's just a matter of getting your bike oriented correctly, threading the funnel into your lever, adding a little fluid to the funnel, and working out some bubbles -- videos are very helpful. I bet that would have solved my problem (relatively) quickly and easily (...of course this confidence will be ruined if the squeal comes back in a couple of months!).

Most of this thread should have been in the Bicycle Mechanics forum because ultimately it seems likely that something simply got funky with my rotors, or a combination of my rotors and the pads I was using, but that this was all just a generic case of brake squeal with nothing of special relevance to commuting.

All of that said, thanks for the many helpful replies and patience as I (hopefully) got this sorted out!