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Why i think he could be alive:if you call the number in the book stanley speaks reverse and the only people who speaks in reverse is bill and the people he controled and when you listen to the flash drive found in the tresure stanly says "my statue" and "shake his hand"
I think Bill is back as a blackbird because when he was "dying" he invoked the name AXOLOTL so he could return as another form. Afterwards, Bill became a statue with his right arm extended as to shake someone's hand to strike a deal. Later on a blackbird landed on Bill's right hand and then went straight to the Mystery Shack and looked into Mabel and Dipper's bedroom.
Hey, um, I know this is a little late, but there's a Film Theory about this (I don't know if you know them or not, but just search, 'Film Theory gravity falls' and it's one of them). It's similar to your theory, Thereal1x1x1x1, but has a lot more detail. Hope this helps!