Hi @trueicecold — thanks for your post & welcome to the forums 🙂
As you astutely discovered, Indigo clones in a fresh copy of the config files from their source inside the Indigo.app bundle every time you start a stack. However, it also checks your stack file (which is also a bundle) and clones it from there instead if it finds one. This allows you to override any service config (or indeed any service file even including the binary itself).
Indigo's override mechanism could certainly be easier to use, and I have a few ideas I'm keen to implement at some point. Until then, the method is as described here.
Let me know how you go!