Container should have negligible overhead, the main problem you’re going to see is where the in/out files are located and shared. Another plus there for docker, can map that volume to anywhere.
If you need a GUI, then handbrake with a web version sounds great, when I did it years ago they didn’t have it.
Since then, I’ve learned ffmpeg and use that regularly and can schedule jobs well now. Definitely more advanced, but more built for server applications.