What I’d like for a configuration language is a parser that can handle in-place editing while maintaining whitespace, comments, etc. That way, automatic updates don’t clobber stuff the user put there, or (alternatively) have sections of ### AUTOMATIC GENERATION DO NOT CHANGE###.

You need a parser that handles changes on its own while maintaining an internal representation. Something like XML DOM (though not necessarily that exact API). There’s a handful out there, but they’re not widespread, and not on every language.