I don't completely understand why to defend a stuck popup being shown as something non-buggy.
Oh, I'm not defending it as non-buggy, I'm saying that I suspect there to be _lots of similar bugs_, as you said this one shows up easily because of the long timing between key down and key up, but it could in principle happen at any place Geany depends on events occurring in order (which is lots I suspect).
And its not just key events, anywhere there is an assumed order the save dialog assumes the document does not change while it is open, running a plugin at an awkward moment changing the document, or running on KDE that does not (or used not) respect modality and allows the user to change the current document resulting in the wrong document being saved, a similar one a while ago was getting an open request from the socket while a dialog was open caused the next operation to be applied to the new document not the original one.