The way I understand this, and I may be wrong.  Is that the M20D recorded signal is taken just after the gain trim setting on each input channel, and before any of the processing happens. 

So, if you set the trim correctly for each channel, it doesn't matter what you do with the rest of the settings on the channel, ie the EQ, Gates, FX, Track mutes, ect.  The recording is already done by the time the audio signal gets there.  This is why each input channel recording is dry (without processing).

This means that you can mute all the channels from the main outs or monior outs if you want.  Those tracks will still get recorded on each separate track.  They will not however be recorded on the Stereo Mix Track, since that recording is taken from the Main Outs.  Basically whatever you hear coming out the main outs, is what will be recorded on the L&R Main Mix. 

I'm pretty sure that the monitor mix doesn't doesn't matter to either the individual channel recordings or the main mix recordings, so you can set up the monitor mix however you want.

So, to do what you want, just mute any channels that you don't want to hear in the main outs.  Keep in mind that they will also not get recorded on the 2 track main mix tracks either since they are muted.  They will however be recorded on the separate track recordings.