UI usage is mostly learned.
Just to be clear, I don't think GTK is the perfect UI system. In my opinion, there is none.
But we need to be aware of those learned habits, metaphors and conventions and build those affordances into our own designs if we want people to use our software efficiently.
A convention often used in modals and other popup windows is to put the close icon in the top right. So putting the confirm button there could cause a user to click it wanting to close the window and confirm a destructive action instead.
Another convention is to put the confirm/cancel buttons at the bottom of a dialogue window. Buttons like those don't normally go in the title/toolbar, and putting them there goes against the top-down, left-to-right way we read things.
Putting things in non-conventional places is not 'wrong' per se, but adds extra friction to every interaction.
Moreover, which users who never used a PC before would be using Gnome?
Yes, it is. There are lots of UX rules backed by research.
Fitts' Law in this case is just one reason why this is wrong.