Mike,
The sub out on the Stage 2 GK-1 does indeed bypass the tube. The reason is that we want the maximum signal we can get at these low frequencies, and the cap coupling of any tube mitigates against this. Since a tube is struggling to deliver the punchy low end bass required in this situation, the sub out is taken from the direct coupled SS front end of the GK-1.
Its volume is controlled by the same pot as the full range signal.
No, running smaller speakers full range will not muddy the mid bass if the speakers are set up with high Fs drivers, which naturally tail off around 50Hz anyway. I use Morel MTMs in this role, run them full range, no problem at all with 'muddy' bass as you describe it. You can run them through a high pass if you want, but I don't see this as necessary.
In fact, for those using active systems, I suggest running the bookshelf speakers full range is a great idea; there should be no bandpass filtering to avoid damaging the sonics (bandpass filters are dynamite for creating weird phasing effects which seriously damage imaging); only a low pass for the sub, and a high pass for everything else.
Hope this is helpful,
Cheers,
Hugh