This is fixed in Gnome 3.34!
But, there was a message added in Synaptic, which is contra-productive now.

if [ "x${USING_WAYLAND}" = "x1" ]; then
    # Running wayland; start synaptic without pkexec
    zenity --warning --width=500 --text \
        "You are using Wayland environment, Synaptic will continue without 
administrative privileges.\\n\
To make Synaptic fully functional, please restart your session without Wayland."
    exec "/usr/sbin/synaptic" "$@"
else
    pkexec "/usr/sbin/synaptic" "$@"
fi


This can be removed! pkexec just works fine now.

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https://bugs.launchpad.net/bugs/1771158

Title:
  Synaptic doesn't open with administrative privileges on wayland

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