Currently, the only way to do this would be to create a new Batch Encode Service with a custom encode setting.
Note: this will override Batch Encode's support for forced subtitles and native language dubbing.
You'll need to use the "--subtitle" flag to include the subtitle tracks.
Batch Encode won't be able to auto-select the cc track so you'll either have know the subtitle track number in advance; or include multiple track numbers.
EXAMPLE (using ATV2 preset):
Code:
-e x264 -q 20.0 -r 29.97 --pfr -a \${audioTrack},\${audioTrack} -E faac,copy:ac3 -B 160,160 -6 dpl2,auto -R Auto,Auto -D 0.0,0.0 -f mp4 -4 -X 1280 --loose-anamorphic -m --subtitle 1,2,3,4,5,6
Tip: If you're doing a whole season or series, they'll most likely be the same track number.
For more info on getting the track number see the HB wiki:
https://trac.handbrake.fr/wiki/Subtitles
I hope this helps!
Thanks!
mac.jedi