I don't think it would work to have him standing in a hole in the deck. Perspective-wise, that would require the hole to be at least 3 or 4 feet further away from the camera. It's not going to look right unless he shrinks proportionally or gets shifted downward in the frame, which you might get away with if you could break him out as a separate element, but you told me earlier in email that he turns and hands a clipboard to one of the other characters. I can't think of a way you would be able to pull that off without the depth discrepancy being painfully obvious.
Let me ask you this: Does anyone enter or leave the left side of the frame, even partially, in any of these shots? I'm wondering if we might shift the live action to the right side of the frame and mirror the angle on the rest of the engineering space. Kneeling Man could then be working on something at the side of the alcove rather than right smack in the middle of it. Just a thought.