ffmpeg has had so many issues in the past [1], it's best practice anyway to keep it well contained when dealing with user input. Create a docker image with nothing but ffmpeg and its dependencies installed and do a "docker run" for every transcode job you got. Or maybe add ClamAV, OpenOffice and ImageMagick in the image as well if you also need to deal with creating thumbnails of images and document.
And personally, I'd go a step further and keep the servers that deal with user-generated files in more than accepting and serving them in their own, heavily locked down VLAN (or Security Group if you're on AWS).
That's not a dumbass criticism of any of these projects mentioned by the way. Security is hard, especially when dealing with binary formats that have inherited a lot of sometimes questionably reverse engineered garbage. It's wise to recognize this before getting fucked over like 4chan was.