IIRC El (El Chiguete) experimented with setting OD2 = 0 with some good results, but as you say, OD1 at 0 means no signal so I don't know why the PG patches are listed like that
One difference with the SS for cleans is that OD2 becomes a compressor level which is only available in the SS voice.
It's good your unit isn't too noisy at high gain
, there are trim pots for OD1 and OD2 and where they are set will have some impact. To check for mods post pics of the internals and MJMP should be able to tell.
Yes the master is the overall level of each patch to balance them with each other for how you play, it doesn't add distortion. The idea is to set your loudest patch and reference everything to that (so you get a good boost going from rhythm to lead etc)
OD1 does attenuate the pre-tube input signal, it controls how much of the signal coming in the input is sent to the first tube V1 (or SS circuit), or as MJMP says the gain of the booster (which I assume is an OppAmp?), higher OD1 levels drive V1 into clipping.