[ajamils]

I have checked the headers and they are set correctly.

I know what the issue is but I don't know what can I do to over come that. As I understand, auto switching happens when they player send the info that content is 3D, which I believe only happens with frame-packed 3D and not ripped SBS mkvs.
When a 3D SBS is played in MPC it just see it as regular 1080p movie (which it technically is) and plays it as normal. On the other hand when same file is played in Native Kodi player it recognizes 3D movie from the 3d.sbs tag and merges both images.
When 3D movie is played in Xbox one, since it a full Blu-ray it has whatever secret ingredient is required for the projector to determine the stream as 3D and it automatically switches the mode.

The KODI internal VideoPlayer has nothing to do with madVR, NCP, or tagging.  SBS.mkv's are not dependent on any stereoscopic settings other than enabling in KODI and your PJ.  Global and NCP stereoscopic do not even need to be enabled for sbs.mkv, only Frame Packed.  I have no idea why your PJ auto switches using Xbone X, which I am unfamiliar with, and not with VideoPlayer?  It should using the KODI player or any other player.  PDVD, MPC and VideoPlayer all auto switch for me using all formats so I know it isn't software limitations.  Did you check the header info stereoscopic value using mkvToolNix?  I think it should be 1 or 11.  Maybe Xbone X doesn't rely on it and KODI does.  Did you try another player like MPC with LAV and madVR via Windows Explorer for further diagnostics?