It does. MP3は普遍的な損失コーデックであり、AACやOpusよりもビット当たりの品質が劣る代償で、何もそれを再生しない. 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 MP3 をマージ rather than before it means the conversion works from the file you finally settled on.
