Modifying the core colors like var(--secondary)

Here’s an example:

It seems that these vars are not configurable. This is the copy / paste from my colors config:

"HT Colors": {
  "primary": "142546",
  "secondary": "FEF9F0",
  "tertiary": "4A7FE5",
  "quaternary": "FBC379",
  "header_background": "ffffff",
  "header_primary": "142546",
  "highlight": "ffff4d",
  "danger": "e45735",
  "success": "009900",
  "love": "fa6c8d",
  "hover": "ebf0f9",
  "selected": "dee6f6"
}

It seems like there must be some other way to set the color vars used by badges, etc.