[read the thread]

IMO, just use one single # as you did at the start, and don't worry about the comment_use_indent comment ~~comment comment~~ (oops, got carried away 🙃).

# as documentation comments in conffiles is most common
#key=value as commented-out default/suggestion is common (many things in e.g. /etc do this)
## is a lot less common, so is #~ indeed.

The one thing you possibly could do is still add a leading # to the \t#comment line, e.g. "if line is an indented comment, add a documentation comment prefix", but that might be an overly specific case to warrant it, and special cases have a tendency to come back to bite you…

and language-specific config files would contain only those values they override to some other value than filetypes.common

Hum, I'm not sure it's a great idea. Some settings make sense to be modified per-filetype rather than necessarily globally, and I think those are the ones showing up in filetypes definitions. E.g. comment_use_indent: it's both a user preference, but also not all languages are happy about it, or their canonical style isn't. Similarly, wordchars has some use per-filetype, where identifiers are not limited to the usual (say, they contain - for example).
So yeah, there surely is room for improvement, but I don't think going whole "no non-overriden settings can ever be mentioned in filetype definitions" is the best move.

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