Finally bothered to print out a 100mm cube which came out to roughly 102.5mm x 102mm. Using M579 X0.975 Y0.980 (technically twice) and reprinting the cube has me within an acceptable tolerance of 100mm.
So I have two questions. First, where is the best place to save the command. Right now it is towards the end of my config.g, but I didn't know if it would impact auto-calibration or not. Second, I assume I am setting a variable with the command rather than applying a modifier, so accidentally entering it multiple times (since it has no feedback in the console) shouldn't be an issue, correct?
Thanks for the help.