What had better happen is that Bill has a couple of adventures, realises "Uh, actually I'm not that into magic puddles mate, sorry" gets turned back into a regular human and immediately bumps into the freshly regenerated Doctor. "It all worked out in the end Doctor, no hard feelings" and adventures with Best CompanionTM resume.
But yeah, was pretty good. It seems appropriate that Capaldi bows out on a really rather low stakes caper, and his David Tennant impression was eerily spot on.