Regarding the malfunctions/sabotage function not being used in NYGM: that is because the Commander file that does that function, randomizedevents.cfg found in the Commander cfg folder, uses hex offsets on SH3 game files to activatate the malfunction/sabotage functions. See the randomizedevents file for examples.
The randomizedevents.cfg file that comes with Commander is based on version 1.4 of the game, including the above hex offsets.
A megamod such as NYGM changes these hex offsets. So unless the mod maker(s) include updated hex offsets for the randomizedevents.cfg file in Commander, Commander will be using the incorrect offsets when activating the malfunction/sabotage option.
Doing that can cause problems with the game files and gameplay.
NYGM did not update these offsets with their Commander files, thus the recommmendation to not use the malfunction/sabotage option in Commander.
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"Realistic" is not always GAME-GOOD." - Wave Skipper 
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