Yeah, its freaking confusing. And the fact that Vegapunk wanted to leave the island always felt like a major red flag, since that would leave his brain vulnerable since we've seen that a few characters can bypass the lasers and that without the bottle factory on Egghead puffing out sky island clouds, the Labophase would come crashing down.
And carrying around a corpse just feels really uncomfortable and pointless now.
If Vegapunk's brain survives this somehow, which I doubt, Vegapunk will likely use Lilith, Edison or Atlas as temporary hosts whenever he wants to speak, but its going to be really risky when Saturn and marine scientists start hacking his brain and start learning everything the other Vegapunks are doing with the Straw Hat.