Already got a reply from EHX on YouTube.
In case someone else needs this info:
““In this setting [i.e. BOOST INDEPENDENT], the GAIN and BOOST knobs are disabled” — does it mean I can’t change the amount of boost

This is correct. The ‘boost’ circuit has fixed gain. The BOOST knob controls how much of the boost circuit is fed into the normal circuit when both are on.

can I bypass the boost in the BOOST INDEPENDENT mode?

Yes, press the BOOST footswitch to bypass the boost circuit in BOOST INDEPENDENT mode.”