Snoop shows the complete visible Tree, but this does not mean, all elements are visible for UIAutomation.
Problem: Not all Controls (and Custom Controls) in a UI implement AutomationPeer (needed for UIAutomation).
So all elements which are does not implement AutomationPeer are not visisble for UIAutomation.
Have you read the chapter
CustomCommands (for White 2.0)?
I have direct access to the developer whcih implement the application I test. If I can't see a custom control and need it for test I ask them to implement AutomationPeer to make is testable.
Hope this information helps.