For config files, we add comment lines with references to issues, commits, comments, conversations, etc.

Here's how a colleague put their comment in a .json file:

  "The_whys": [
      "https://repomanagement.com/GoodCorpHere/XXXXXXX/issues/XXX#note_XXXX",
      "https://repomanagement.com/GoodCorpHere/XXXXXXX/issues/XXX#likely-parts-and-draft-fix",
      "https://repomanagement.com/GoodCorpHere/XXXXXXX/issues/XX#likely-parts-and-draft-fix"
  ]

But you make a good point. It could be done by adding an agreed upon field in TOML/JSON/YAML config files that would contain warnings, but not for now.