I like the approach to tell the user that some global settings will be overridden by projects to reduce confusion.

When changing tooltips, it might be easier to change the original tooltips in the Glade file by simply 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.

Another solution could be to show some sort of symbol, like warning sign or the like, next to those settings which can be overridden by projects in the preferences dialog. Those symbols could then have a generic tooltip.

Changing tooltips of all settings which can be overridden is probably a tedious work and might make the code less readable for little effect.

Just my 2cents.

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