Yes — MOVはProResとリアルアルファチャネルを持ち、H.264プロファイルに再符号化すると、両方を無音で捨てる. It is the kind of thing that explains why a file looks right in one application and wrong in another.
透明度の決定は,透明度の変更を行う段階である。 That is the step most people actually came for, and doing it after MOV を回転 rather than before it means the conversion works from the file you finally settled on.