I added it early on because a number of people who use MO2 were complaining that their MCM settings weren't being saved.  Apparently when the game was run through MO2, the ini file either was not being created, or was created in the wrong place.  Adding the file to the archive fixed that.  I don't know if this is still a problem, I don't use MO2 myself.   I'll look at making the ini file optional, I agree that it's annoying to have your settings overwritten each time.
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