I will ask ritsuka but iirc he said its the same as the optimization in HB. ritsuka is the Subler dev as well as a dev for HB. That said they both us libmp4v2 for muxing etc.
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Just talked to him, its the same. no difference.
Thanks for doing that. I think I had read somewhere that someone recommended using Subler for optimization because it used v2 and Handbrake used v1. That clears everything up.