For work files some of the higher-level folders (shot, task) still have to be registered in Shotgun, which I suspect New File might also do (someone more knowledgeable should confirm). File Save does that certainly.
The Unknown user is a known thing on Windows, I think file ownership is not properly reported for work files by Toolkit (Windows ACLs are weird). Couldn’t find a relevant forum post right now.
This might be relevant to you Creating user sandbox folders without needing the user to work on the task