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.
Yeah, that provides no guidance to users.
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).
Which kind of argues against my suggestion above of having all of `filetypes.common` in each filetype file commented out.
(the "usual" is rapidly becoming Unicode, eg C++ can now start with [XID_Start](https://www.unicode.org/reports/tr31/#Table_Lexical_Classes_for_Identifiers) and continue with zero or more [XID_Continue](https://www.unicode.org/reports/tr31/#Table_Lexical_Classes_for_Identifiers) and C is planned for version after C++23 IIRC, but thats another issue [@elextr clambers down off his "not all languages are C" soapbox] )
So ultimately I agree with @b4n that the simplest solution (add `#` to any line not starting with `[`) is best.