It's actually really confusing and has some plot-points in it. You see, unless I'm misunderstanding this, the Walrider is nonsentient. It's just a cloud of nanites with the brain of a human. Ingame, that human is Billy Hope, until the very end, where Miles kills Hope and unwillingly becomes the brain of the Walrider. However, the Walrider ITSELF possesses Miles, seconds AFTER Hope is killed, so I have no idea how the Walrider was sentient enough to force Miles to become its host (ei, possessing him). Maybe it has a few sliver of sentience.
We don't really know for sure. Maybe an Easter Egg or Document in the next Outlast may be present to explain the current conditions of Waylon or Miles. Maybe in that scenario it's a new company who have been working with MURKOFF? We don't really know for certain, but you can make up your own theories about it, which may be relevant on the Outlast Fanon Wiki.
My take on it is, right s Billy was dying, he was controlling the Walrider and making it toss Miles around a bit. But right when Billy died, the Walrider was released from his control, and went to the next ready 'Variant' . . . Miles. Keep in mind he'd been tortured and seen enough horror at this point to be another perfect host for the Walrider, so I believe that because of this, the nanites were drawn to fuse with Miles.
And at the end of Whistleblower when you see Miles walking out, I believe he had complete control over the Walrider. Whether he as sane enough to use it for good instead of evil, that I can't be sure of. At best, he was neutral but teetering dangerously on the edge of total insanity, though he seemed in control of his mind enough to let Waylon go. However, whether at the end he gave Waylon in his jeep a little nudge to escape, or the nano swarm was closing in on Waylon and the jeep to kill them, I'm not sure of the answer. That's why I say Miles is neutral at that point.
But then again, this is just a theoy. . . a game theory, lol. /shoutouttoTheGameTheorists.