This is a design problem.
There should be no such thing as "Save as..." dialog.
Users expect all the file manager functionality from the dialog, so
effectively the whole Nautilus gets recoded as a "Save as..." dialog,
doubling the effort, bugs, fixes etc.
We have it all coded in Nautilus, so why cannot we just use it?
There should be a "save as" mode in Nautilus. When the GTK+ dialog is
called, it should check if there is Nautilus present (it does that
already, to show the mime icons AFAIR) and call it to open a window in
"save as" mode and get the save path from there.
If not - show the old plain GTK+ dialog without all the fancy stuff.