Have tried many things to get 3D Blurays to work as follows.
1. There is one other tool that supports creating an mkv with the mvc setting, however requires special player software to play it back and i could never get it to work right as it would always show in 2D not 3D. Tried using Steroscopic player with no success. Documentation says to open the main movie ssif file contained in the Stream\SSIF folder (where the 3D part actually is). Tried that and it still played the movie in 2D
2. Did the rip, then the conversion to either SBS or TAB mkv with mixed results. Basically had to manually set the player to either SBS or TAB and always had to set the tv manually into 3D mode (SBS or TAB) even then results were not that great and it was very hard on the eyes. This solution was also dropped.
3. Came up with the final two solutions that works best and reliable and works all the time using PDVD, and that was to either create an full ISO in clone mode (which for sure copies the data in the SSIF folder) as i'm not sure yet if you do copy as bluray 3d that it actually copies the SSIF folder with the SSIF files (I know many versions ago FAB would create an empty SSIF folder and was told by support to always use clone mode, but that may have changed by now).
Then mount that cloned folder for the ISO and invoke powerdvd. Menus would come up and i could select normally in PDVD. Since the movie is frame packed my TV is automatically put into 3D mode and all very seamless. One thing if i recall this correctly was that in the PDVD settings i set the option to play 3D movies in 3D always. This is very seamless as there are no manual adjustments i have to make to the TV and/or player. There was times though that for some reason the lip sync was off just a tad using the full ISO. For most documentaries this is not a problem since you don't see the person actually talking
4. Solution 2 (One i use now), After the clone to iso, then use winzip to expand that folder into the raw folder layout within a folder on your movie drive. Then create miniso in that folder and then double click it and let pdvd do the rest.
For my particular situation i use Kodi as my standard movie library player for 2D blurays ripped to mkv's and for bluray 3D use PDVD as an external player to Kodi for bluray movies that i have planted out the full BD Structure in 3D. Once Kodi finds this external player then based upon the my external script settings i have the script invoke PDVD Cinema player instead and the script passes the path to PDVD and away it goes.
So for Avatar i have kodi play the 2D extended version and then have kodi invole PDVD to play Avatar 3D. Once Avatar 3D is started my TV goes autmatically into 3D mode and once movie is over TV reverts back to 2D mode, the same way it does with the actual disk itself. Hope this helps you