I don't know how to answer this, but i'll just tell you something whether it helps or not I don't know.
M3 has a "Boot.nds" file so once i open in DS mode it goes straight to M3, if you could get it to do this with a boot file, then after that in settings you can just set it up to switch on and go to the DS game. But yeah I don't have a boot file for linux ;-/
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