Upstream has provided a fix:

commit 91ff70db0c49d22fac1b249bd16949978406c271
Author: Mathias Nyman <mathias.ny...@linux.intel.com>
Date:   Mon Aug 29 14:45:17 2016 +0300

    usb: hub: Fix auto-remount of safely removed or ejected USB-3 devices
    
    USB-3 does not have any link state that will avoid negotiating a connection
    with a plugged-in cable but will signal the host when the cable is
    unplugged.
    
    For USB-3 we used to first set the link to Disabled, then to RxDdetect to
    be able to detect cable connects or disconnects. But in RxDetect the 
connected
    device is detected again and eventually enabled.
    
    Instead set the link into U3 and disable remote wakeups for the device.
    This is what Windows does, and what Alan Stern suggested.

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https://bugs.launchpad.net/bugs/1239087

Title:
  Safely remove is not working (or broken) in Gnome Disks

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