It would be very helpful when arranging a song to build up a pattern track by track – e.g. initially play pattern 12 with only tracks 1,2 then next time around add in 3,4, etc. Is this possible?
Simple answer - no, there is not mute in song mode.
More expanded answer - no 
BUT … you can just add a new slot wherever you need it and copy the tracks you want into the new pattern you just added in between somewhere. Hit Rec in Song Mode and copy/paste individual tracks or a selection of tracks around.
Oh I think I see… Insert a new slot, and then choose an empty pattern and then copy tracks from one pattern into my new empty pattern. Song mode is a shortcut for cloning portions of patterns into new patterns. This sort of works, but when I select an empty pattern, the pattern length is only the default length, even if I copy and paste longer tracks into it. Still not a great workflow.
I do just wish there were a way to mute individual tracks at the song level. The UI already shows us tracks muted at the pattern level. They could just replace the “Undo” button with “Mute/Unmute” since in this context Undo almost never works 
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This is actually a known bug that has snuck into the last firmware. I’m sure that will be fixed with the next update. 
This actually already has been wished for twice so far 
. Sadly it was already declined the first time around:
To be honest, I don’t really like how the Mute function is implemented so far. I recently bought the Tracker, and it’s driving me crazy. In Polyend Play, everything in this regard is done brilliantly.
Here, for some reason, we can do Solo in Master mode, but we can’t do Solo in Pattern mode.