My personal feeling is that we shouldn't use them in our conffiles,

Agree. I think that apart from the reasons mentioned above, it just looks nicer in the conf file when all commented-out lines start with #.

but that we should support them in the file type; I don't see any reason why to limit this, is there really valid cases where it causes problem to support it?

I don't have a strong opinion on this. There are two possible views:

Display all possible conf files nicely syntax-highlighted.
Encourage users to use the safest conf file format possible by not highlighting a possibly invalid format (the specification here https://specifications.freedesktop.org/desktop-entry-spec/latest/ar01s03.html doesn't say anything about leading or trailing spaces so it may be implementation specific).

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