It does. WAV は非圧縮 PCM: ビット精度と編集可能、ステレオ分あたり約 10 MB. Matching inputs take a fast, lossless path; mismatched ones have to be reconciled to a common format, which is slower and costs one encode.
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 WAV をマージ rather than before it means the conversion works from the file you finally settled on.