I should have responded earlier. I can confirm that CloneBD is working now.
I can clarify. There's no official spec for MKV with UHD so it's a bit of a fluid situation right now. However, I've had lots of success with mine. The caveat is you will likely never get Dolby Vision support (MKV has no spec for it at all and it's a closed format anyway so no one knows how to play it) in an MKV container. It will do HDR just fine though. ATMOS is all good. I HIGHLY recommend a player that uses madvr and lav filters if you're going down this path.