Ok, I experimented all the way home and have some answers!
Short version: It is software limited, and Reid was right, lowering the low voltage limit resolved the issue. There might be normal battery charge degradation and cold weather also contributing, but it's clear that the issue I was describing is due to the low voltage software limit.
But something interesting may be going on... read on for long version:
I was in boost level 1 the entire time. I started with the low voltage cutoff at 42V.
At the start of the ride, resting voltage was 48.0V (50% charge). When I started pedaling, the pedal assist consistently caused voltage to dip about 1V, to around 47V. If I then applied the throttle, it would drop another 1.5-2V, to around 45.5-45.0V. Basically, if I used both pedal assist and throttle, I saw a drop of about 3V.
This behavior was consistent until resting voltage got down to around 46V. Then, when I started pedaling, the pedal assist remained very consistent, causing about a 1V drop, to 45V. However, if I tried the throttle it became noticably less powerful, and would only cause about a 1V drop, to around 44V, instead of the 1.5-2V drop it was doing prior. So, total voltage drop with pedal assist and throttle was around 2V, and throttle was sluggish.
Then, when I hit a resting voltage of around 44.5V, I could start pedaling and get the same 1V drop to 43.5V, but the throttle basically had no effect, and the voltage didn't drop any further at all.
Then I set the low voltage cutoff to 40V (resting voltage still 44.5V). At this point, I could pedal assist for a 1V drop to 43.5V and the throttle was instantly restored to full effect, causing a drop to around 41.5V.
My half-baked theory: With my low voltage cutoff at 42V and a resting voltage of 46V, I would have still expected full throttle (pedal takes me down to 45V and throttle only to ~ 43V, well above the cutoff). BUT if the low voltage setting of 42 is really acting like a 42.X cutoff (meaning anything below 43V would trip it), then all of my observations start to make sense. With a resting of 46V, pedaling taking me to 45V, that throttle would cause a momentary dip just into 42.9V territory, cutting it out, and maybe it's cutting in and out intermittently as I hold throttle, which gives me the overall effect of "half throttle" or sluggish throttle.
Then, when I got to resting 44.5V, it makes sense that the throttle basically wasn't working at all, because pedaling takes me to 43.5V, and then at that point I'd only be a short distance from the 42.XV cutoff so the throttle would basically instantly cut out.
The fact that I could set the low voltage limit to 40 and immediately the throttle would cause a dip to 41.5V and give me full power confirms this is primarily a software issue.
So, my plan is to set the limit at 40, which should give me full throttle down to a resting voltage around 44V, and I usually don't get that low on my normal commute. A resting of 44V is > 30% charge, so this seems ok in terms of battery life.
As the weather warms, I'm curious to see if pedal assist causes a less than 1V drop and/or throttle causes a less than 2V drop.
Thanks all!