Just coming of a contract myself, similar situation.
I made some early and somewhat feeble attempts at pure ffmpeg, but the matrix to map working handbrake -> ffmpeg was too overwhelming at the time.
I'm revisiting now since something changed in 1529/1553 that breaks AC3-based encodes on my N1100 and the 2000C, but not on the N1101: 1-2 seconds after selection, the dreaded 'format not supported and/or corrupt' then punt. A brief mp4 survey may suggest that AAC-based encodes work on all three models, AC3 only on N1101, and all three are on 2.9/1553, same LAN, same source.
I really like quality audio so now that I'm facing re-encoding, revisiting ffmpeg looks more attractive.
I'll post again when the test cases and specific matrix of what works/doesnt is complete. A few days at the most.