I'm not sure if it's a common way to use it either. I've only used it for installers myself so far.
Ha, ha. It seems, that most users apply only one half of RunBySmartScreen.
RunBySmartScreen works like
on-demand "SRP + Forced SmartScreen" (although it does not use SRP). So, when the user opens a file by pressing Enter or the left-mouse--click, the file is opened normally. When he/she uses the right-mouse-click and chooses RunBySmartScreen, the file opening is restricted and the alert is displayed (for unsafe files). In this way, the user can apply two security setups by simply choosing between normal file opening and opening it via the right-mouse-click RunBySmartScreen entry.
If you open in MS Office or Adobe Reader a document from a flash drive, then it will not be opened in Protected view. If you will do it via RunBySmartScreen, then the MOTW is added and MS Office or Adobe Reader will open the document in Protected view (as if it was downloaded by the web browser).
MT members usually pay attention to file extensions and do not open files with unsafe or unknown extensions. So, they can use only one half of RunBySmartScreen.