HandBrake

I am not sure if there's some limitation but it seems like it would be pretty easy to support. I would like to be able to set the first subtitle track as the "default" and have that save across presets. You can force burn in on the "Selection Behavior" but not the "default"

If someone is actually able to accomplish this please let me know but the only way I can see to do this is load the files I want to encode. Select the preset, then manually select the subtitle as default.