Not sure if this finds its way into the to do lists of the developers as this is a very special request. I actually never heard about mkv videos with flac audio.
But in the meantime you just could use other tools to join video and audio externally. MkvToolnix is a free portable app to do such things. I just took a look into it and it also allows flac as audio source.
That means you could easily export video and audio separately to join it right after within seconds in MkvToolnix. I use this tool very often, its easy and fast.
https://mkvtoolnix.download/downloads.html
If you have further question. Just ask!
