It would be nice to set a target format. I.E. mp4 or mpv over mkv. Remuxing is very fast and does not require heavy processing. Rebox.Net is a good example of simple Mkv to mp4 support. But remuxing engines are available for just about any format.
Not likely to be supported directly, but executing custom scripts is something we’ll be looking at: https://trello.com/c/mCJyYeZl/122-custom-notifications-scripts-similar-to-sab-post-processing-scripts