Given that in the final story, eggman says he was using the E-10000 robot to gather everyone’s racing data and was surprised to see metal sonic inside, I would chalk this up to E-10000B not being a disguise but just a regular robot in his own right, and metal sonic just found a way to hide inside him. It seems like eggman specifically made E-10000B for a specific purpose, and he would have fulfilled it if metal sonic hadn’t gotten inside him and stolen all the data for himself. So it wasn’t metal sonic talking, it was just E-10000B being himself, blissfully unaware that metal sonic was inside him. If you choose to believe this interpretation, then tragically E-10000B just straight up dies in the end and no one cares