My guess is that Billy is not a host (thus he passed the scanner), but a version of his project.
The goal wasn’t to make hosts real, but to turn real people into hosts. Providing them with a physical body so their minds could live forever.
It could explain why he’s been able to survive so many gun shots. Why he may not be as scared of death as you’d expect. And why most recently, they twice showed him looking to his arm - once after the party and once at Westworld. And just as he said, he didn’t belong in the real world.
This could also loop into why he’s been so determined to figure out the game and Ford’s plan. There may be a major gap/obstacle to true success and he believes Ford has the answer.