Yes make mkv can run on hexos but at this time it will have to be installed via the underlying truenas interface. However i suggest just running it on whichever machine is stronger for convenience purposes.
Here is a guide to install it on truenas
https://www.reddit.com/r/truenas/s/FyNpLmWfYi
In case there is any confusion still on this topic, a local UI is coming...100%. We actually have already begun work (we have a docker container with the UI running at this point, but it's not fully functional yet).
I hope Home Assistant integration is pretty high on the 'To-Do' list given its prevalence in the community and seemingly frequent pairing with TrueNAS. It'd be my first request as far as home automation handling goes after some searching