Oh jeez, I'm an idiot. I finally got it. Thanks everyone.
Of course it's in Appdata. I thought I had indexed everything and when the default config didn't show up when I searched for it I thought it was somehow hidden in the program.
And I didn't put the default .conf and then the mc2 conf to use the game settings in the shortcut.
"C:\Program Files (x86)\DOSBox-0.74\DOSBox.exe" -conf "C:\Users\\AppData\Local\DOSBox\dosbox-0.74.conf" -conf "D:\DOSConf\mc2\mc2.conf"
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