Character mistake: When the plane is speeding down the runway at the beginning, a female flight attendant is seen walking, and Kyle is seen buckling her seat belt. Everyone would have been sitting down and buckled in at this point.
Character mistake: An air marshal would not give such leeway to someone detained for such disruption. The person would be detained and immediately routed to the nearest airport for investigation or arrest.
Answer: The hatch they climb into is the hold of the plane, i.e., the section with the coffin, the car, and all the other luggage in. It only appears small because of the way it is filmed. As Kyle would have known, it would have been extra strong and reinforced, as it was a break in two sections of the plane.