If Full-SBS or 4K video is rejected by many hardware players, it's due to the relatively low capacity of their graphics buffers and/or the speed of the rendering engine. Every hardware has its limits, and currently most 3D TVs or projectors support only Half-SBS (or Half-T&B) in 1080p (but some can support Full-SBS/T&B in 720p).
Also, for totally different reasons, it is currently not possible to convert the subtitles to 3D in Full-SBS or Full-T&B format, because the graphics format (BD SUP and DVD VobSub) are made for "standard" resolutions like PAL, NTSC, 720p or 1080p, but not for left+right combined views such as Full-SBS (3840x1080). It is however still possible to hardcode the subtitles on the video.
So, be sure to know what you are doing. If you untick the Half option in the last tab, the compatibility of the MKV with most hardware players will be very low, and you won't have the possibility to include 3D subtitles. But if your hardware supports it, the video quality will be very good, especially with a low CRF like 17.
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