Well, I had a chance to test it.
Without starting SH3 Commander, I loaded up my career and found that ahead flank was still broken. So any malfunctions set by SH3C do stay if you don't launch the game again with it.
I then quit the game and started SH3 Commander, unticked the 'malfunctions' option, and used it to start SH3. Loaded my career once more and ahead flank now was restored, so removing the option mid-patrol does actually remove the malfunction. So won't be using your suggestion HW3, sorry!
It seems the best way to go is definitely to
only use SH3 Commander to launch SH3 when you start your patrol, and launch SH3 from the regular shortcut at all other times. Removes any mid-patrol randomisation of thermal layers and escort patience when hunting you, but at least each patrol will use different settings to the last. (Unless you don't use malfunctions/sabotage, in which case it doesn't really matter!
)