So now I'm dicking around and things are starting to get interesting.
I inverted the B channel signal and set the scope to add... and the difference was quite stark. This difference changed significantly as output on the function generator was increased, but remained almost identical as the frequency was changed: it was like a sine-wave squishing and expanding apart.

I disconnected the power resistors and measured their resistance with the Fluke.
I came up with 8.22Ω and 8.20Ω so they're decently close to one another, then I swapped them around Left/Right, cut off a bit of wire and reattached the cleaned wire to the binding post yielding these new different results:


Weirdly, after cleaning and swapping around the resistors, the outputs look almost identical, Vp-p wise. The behavior of the difference of signals remains the same (changes on output from signal generator, squishes with changes in frequency).
The probes are on 10x for this. The I'm thinking it might not be stupid to open the amplifier and start probing to find where that difference of signal might be coming from, but first I think it would be smart to set the biases appropriately.
One final note worth adding (I am writing notes to myself as well as everyone else, I'm not expecting everyone absorb and interpret every detail on my behalf!), depressing the "Auto Class-A" button makes no difference in the signal. None. I tried at different power levels, low, high, different frequencies, measuring the subtracted signals, I saw zero change to the signal.
I think I'm going to open the amp up and set the adjustments according to the manual... One final thing I've noted, I need longer probe cables for my fluke multimeter!