Francesco, We totally understand the frustration in regards to controlling the visibility of model tree elements and better seamless integration of Pro and Control is being actively reviewed for development. The issue of the 3D model not synchronizing may be due to the large SP file size limitation that was identified with the current versions, and will be fixed for the next release. If you haven't already, I will suggest sending your files/project info over to synchrosupport@bentley.com for further review.
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