Did you completely miss the part in that conversation where they talk about the "interface" being done soon, and that the MC was a good candidate for it?
To me that implies that the MC is somehow being controlled, not doing the controlling. This is doubly compounded when you use logic and think about how he saw his body (as through a camera lens) and was unable to move either during that scene, or during the scene with Megan and the other girl. It's almost as if..*gasp*.. his consciousness had been hijacked and uploaded into a computer system that he had no control over!
You know the brain activity that designates us as living beings is just electrical impulses, right? So, in a sci-fi setting, why wouldn't some sort of tech be able to copy that, or 'upload' it, like you would copy or move a file from one PC to another via USB?
With that being said, I agree the writing during that whole part could be made much clearer. I don't know if it was poor writing, or how the scenes 'jump around' due to bugs, etc, there but it was a little hard to follow. I think a scene or two of exposition would help bridge the gaps in the story to ensure that people understand what is going on (or alluded to be going on) a bit better.