I was not aware that raw2cdng supports 10 and 12 bit. I never use it, just thought its so long since Chmee touched it.
If you want to convert straight to a compressed codec, MLVProducer is very good, it has many options.
You were asking about raw2cdng so I assumed you were looking at a DNG converter. If you want high quality DNG's, I think the Script Danne made is the best choice. For as far as I know, currently Danne's batch script is the only way to batch process MLV's with Darkframe Averaging on a Windows machine.