It can, and it does work like that, especially if Young Xehanort of all people can be there.
I think it can be assumed that Vanitas' heart became one with Ven's again, especially considering how the beginning of BBS foreshadowed Ven reclaiming his lost fracture. With Nomura's quote in 3D Ultimania, he didn't say that Ven's heart was reacting to Vanitas, but that it was reacting within Sora's heart, most likely in response to YX's manipulation. If anything, I imagine Vanitas was and always has been within Sora, and could partially manifest himself through Young Xehanort, who himself is a portal for other vessels. That he still exists in some form is undebatable, though, and how he'll be brought back will most likely be important in KH3.
This pretty much sums up my thoughts on Vanitas in DDD, and his position as a possible vessel: