I recently ripped my LOTR Extended editions using the directions found here. I ended up with three very large (60+GB) MKVs. All three ended up playing perfectly, streaming from my unRAID server to my Dune Smart H1. It was a little time consuming, but to me the end result was worth it.
I ripped Game of Thrones with DVDFab, but my output was passthrough mkv. No problems that way. Only thing I ended up doing was stripping out the subtitles and running them through BDsup2sub and ripping out the forced subtitles only. I then remuxed them back into the mkv and set the default to forced. Plays back perfectly.