Could you look in the list of process what url was called exactly for
gdebi? maybe it's using a x-desktop: url which gdebu doesn't handle?

** Changed in: nautilus (Ubuntu)
   Importance: Undecided => Low

** Changed in: nautilus (Ubuntu)
       Status: Confirmed => Incomplete

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https://bugs.launchpad.net/bugs/1807761

Title:
  Unable to install deb-file stored on Desktop (which is controlled by
  nautilus-desktop) with GDebi

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