Hi Bob,
When using "bypass mode" with an analog input, both the main and sub signals should be full range.
Here's the bass management matrix for analog intput (and for completeness,
here's the digital BM matrix). The thing with analog processing is that I don't want my signal to be sampled into the digital domain. Say I've got my favorite turntable or an uber-expensive DAC -- I want that signal just to go straight through, with no digitization.
So although the mains may be set to "small", since all this BM stuff is applied in the digital domain, we can't have it when using analog inputs that we want to preserve in the analog domain. They're allowing you a means to do all your own bass management if you're into that kind of thing.
As to your #1 plot, I'm going to try to repeat that myself. It may be another bug...