you have to fix the indentation because if not then the document won’t work or mean something completely different

Whitespace has no meaning in json. You can indent however you want, or not at all.

I'm assuming you're running into issues because you're writing json in a yaml file which does care about indentation, and you're only writing json in yaml to get access to comments.

In which case it circles back around to: why not use toml? Whitespace formatting doesn't corrupt the file, and it has built in comments.