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Can Media Encoder (or any other Adobe application) perform functions that ffmpeg and Handbrake do, regardless of whether it takes longer or uses more resources, etc.?
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I'd say it's better than both, but try it for yourself and report back.
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Can you be more specific? What ffmpeg or Handbrake functions are you looking for?
Can AME add toggleable subtitles to a file like Handbrake can? No.
Can AME natively export H.264 using x264? No.
AME can export to many more formats than Handbrake.
With a simple line of code ffmpeg can easily combine an audio stream and a video stream from one file into a new container without encoding a new format.
Those four things are pretty different from one another, so what is it that you're hoping the Adobe apps can do?
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AME cannot handle VFR.