Jim,
You can close a window and prevent it from reappearing with the ORM designer the next time Visual Studio is launched. However, the window will reappear the the session after that. The tool window visibility is managed completely by Visual Studio--NORMA just responds to a request to populate the window contents--so I consider this a VS problem. I will admit, however, that I haven't spent a lot of time researching the issue.
As for ID/id/Id and other reference mode patterns: the long-term plan is to move all reference modes and other information (specifically intrinsic data types and units) into an editable 'machine.orm' file. To keep the .orm files independent, any data from this file will be copied into your model on use, but the dropdowns for this like 'reference mode' will be a combination of the elements used in your model and the elements defined in the machine.orm file. The distinction between intrinsic and custom reference modes will be eliminated, and you will have full control over which elements you want to use on your machine. Merging intrinsic/custom reference mode will be done as part of a datatype revamp that will allow multi-valued value types, custom data types with facets (size, length, etc), and unit association with value types. Sorry, I can't give a timetable for this right now, but it is moving up the list.
-Matt