In Help, after/below Save geometry only is stated “This is similar to exporting the objects. A new file is made, but it does not become your active Rhino model.”
The same should be stated (multiple places) for when Save plugin data is disabled.
Also, should these issues be closed since Save plugin data was added to V6’s Save dialog?
https://mcneel.myjetbrains.com/youtrack/issue/RH-20992/Add-SavePluginData-to-UI.
https://mcneel.myjetbrains.com/youtrack/issue/RH-24428/SaveAs-without-plug-in-data