The function "Mute" in Polyphone is only here for a testing purpose: it is not linked to a key and is not saved in a file.
The feature you are talking about, introducing a conditional start of a sample, is unfortunately not included in the soundfont format 2.04. Unless this format evolves, this will remain impossible to do.
What you can do however is to provide 4 presets in your soundfont, one for each oscillator, and then add an extra layer processing MIDI signals such as jOrgan so that you can combine the different oscillator the way you want.