Well, as far as I know this is how it is supposed to work. That kind of privileges are handled by policykit, which has a differentiation between local and remote users. And local users have more privileges than remote. When you start a new session with X2go you are definitely remote user, while with VNC you are kind of local (for policykit at least).
You can override that with a bunch of xml config files, but someone has to analyze all required privileges and for each one create a config.
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