When you use this mod with the X2WOTCCommunityHighlander, you can prevent these augments from being applied to your soldiers automatically, both on character creation AND when applying a new armor set. Here's how.

1) Subscribe to X2WOTCCommunityHighlander
2) Subscribe to this mod
3) Enable both mods in the mod launcher. Make sure the highlander is loaded first in your load order.
4) Run the game and open Options > Gameplay tab
5) Set the slider for 'Augments' down to zero and Save
6) Load up a save or start a new game to test it out.

I use this mod alongside the Gravely Wounded Prosthetics mod. My personal preference is that these augments are only automatically applied after an injury, not at character creation or when applying a new armor set. I apply the augments to my wounded characters manually, after changing/upgrading their armor.

There's a bug in the base game where changing to a new torso armor for the first time does not respect your DLC sliders in the Gameplay menu. A recent update to the highlander fixed this behavior. The highlander also fixed the bug where setting the slider to the minimum value resulted in some body parts still having the DLC content.