I finally discovered why my text color had reverted back to vanilla's dark colors. The file name is kenshi_colours.xml and I've found it used in Shidan's Tweaks & Fixes and Unofficial Patches for Kenshi to add an additional item-grade color.

Placing Dark UI + Shidan's T&F patch bellow Transparent UI (etc.) and either of these mods (or any other mods that include a kenshi_colours.xml file) will allow you to order them freely without this specific issue occurring.