Rudder...rat,
Sure, I agree that you can't keep an internal reference to an absolute position, or distinguish whether you're on a vehicle that is slowing down or going downhill. The pitch-up illusion on acceleration on take off in an airliner is by 10-15 degrees or so.
However, when you stand up out of a seat, you can still tell whether the floor is apparently sloping or not. You can tell whether you have to grab the seatback in front and pull to climb into the aisle, or push against it to slow yourself.
During the pitch up (which woke/roused the Captain?), had he been on his feet, he would surely have felt himself to be heavy, and known there was upward acceleration, as in an elevator. When the aircraft was reaching its maximum height he might have been felt a bit light. As he put one foot in front of the other on (the short?) way to and into the cockpit, would he not have noticed whether he had to haul himself up a slope, or was rushed forward downhill? While not being able to perceive absolute motion, he surely would have been able to get a sense of an unusual attitude, unless the acceleration and attitude were unfortunately aligned to make things feel normal when he was on his feet. Or maybe his heart was pounding, and the aircraft was shaking, and he couldn't get any such subtle cues?