You can skip the MakeMKV part and directly encode through Handbrake if you add the required libraries (libaacs, libbdplus) in your Handbrake install directory and grab decryption key database (which I won't link here). You can do the same with commercial DVDs and the libdvdcss library.
Then it's just a matter of opening the disc directly in Handbrake.
I use ffmpeg to batch convert ripped files. Decoupling ripping from transcoding is more efficient for me. I can get all the ripping done as fast as possible. Transcoding takes a lot longer.
Then it's just a matter of opening the disc directly in Handbrake.