I did let it go. The whole thing. I work mostly on groups of small files and this bug has put such a crimp on the workflow that it is no longer worth it.
There may be logic in the feature but the implementation is FUBAR.
For starters, the distinction between open/save and import/export is now broken. I.e. if I could use Open to get the file, I expect to be able to use Save to put it back. That is pretty much how every other piece of software works.
But worst of all, it induced an endless litany of dialogs. Not just when "saving", but originally also when closing as GIMP considered the file dirty unless saved it to its native format. The Overwrite kludge, IMHO, is a sign that this thing is broken.
And lastly, the export dialog does not retain settings. That's especially lovely if you're working on a batch of JPEGs as most settings are hidden from view.