You make a solid point, but I feel like of all people, Scotty could rig up a force field to block off the front section. It’s even got a nice little lip around the inside just behind the cockpit.

Overriding the safety protocols and interlocks to open the hatch mid-flight and re-close it on the other hand…

I feel like he got things figured out.

(also my headcannon is that there are fold-out facilities on all shuttles, similar to how they showcase bathroom use and hand-washing in Firefly)