MKV is just a container that typically contains h.264 and h.265 video. Most iPads have a dedicated h.264 decoder (new ones have an h.265 decoder as well). I'm not sure if they all support h.264 encode as well... but I believe they do since performance is so good when shooting video.
Anyway, Apple has never supported the open MKV format and likely never will. They are all about MP4 and MOV. Potentially a third party App could support saving to the MVK format, much like how VLC supports MKV files for viewing. Something you'd have to research.