appending a note like "this setting might be overridden by open projects" or something like this.
I guess users know when they have a project opened.

Yeah, thats easier, but the tooltip doesn't show unless the user hovers for a period, so the insensitive is important too.

Another solution could be to show some sort of symbol, like warning sign or the like,

Trouble is no symbol is an obvious "this is overridden" especially that new users will understand automatically, and its new users who need the warning the most. Thats why setting insensitive is useful, it makes the user stop and think for a moment :)

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