As the Title said, 3D options (seted in Kodi OSD Videosettings) dont have any effect on 3D Youtubevideos.
Here’s a Example to test:
In this Case Kodi shows both Pictures (sidebyside) No mather what i set In the OSD-Videosettings.
Tested on Kodi 17 Beta 6 (Nightly) on Windows 10. (Plugin V. 5.2.1 if this helps.)