Very much so. 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. That determines both the headroom available and whether the saving costs you anything in fidelity.
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 を圧縮 rather than before it means the conversion works from the file you finally settled on.