One more hint concerning 2: I guess you are using the EasyPanel add-on, which contains a dependency to the ModeHandlerTemplate allowing several versions. In general, when an object contains a BaseRef or Using allowing several versions, Object Browser selects all applicable versions of the referenced object. It should not select objects referenced as "Dependency", but it currently does. These two points are already in our backlog. What I cannot reproduce is that the ModeHandlerTemplate wasn't even selected before it was downloaded. When I select the EasyPanel, several ModeHandlerTemplate versions are selected.
And another hint concerning 3: The import from the ObjectVersions.xml does not consider the object versions. It will always download the latest version. It's also on our list to improve the function so it tries to download compatible versions at least. But still I am not sure if the function would be a good replacement for backing up the Std folder. Maybe it is good enough for a BaseStation project if you don't care if the exact same object versions are used every time.
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