At a guess I'd speculate that you could remove the medal references from the config file and have SH3Commander replace them on the dates they become available, that way they wouldn't be awarded in game and SH3 and Commander would be in synch.
On the other hand, there's a good chance that this would cause a crash of some sort as I'm sure Jaeson would have written Commander that way from the beginning, instead of having their systems independent.
It's not something I'm going to delve deeply into as I manage just using Commander for my crew awards, and edited my files to make my own awards a lot harder to come by.
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The owl and the pussycat went to sea in a beautiful pea-green boat.
It only took one T1 eel to convince that boat not to float.
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