That's just how it's designed-- OBS is using the program as a video source, just like it would a game or something. So it just sees what's going on in the program (minus whatever color your chroma key is filtering out). To hide the UI from OBS would be to hide it from you as well.
What you can do instead is you should be able to assign state changes to a hotkey so that you don't have to tab into the program at all to change it.