Where was he in between

The capsule pod was an artificial simulation created for his mind to rest between source code jumps. Also a place that Somewhere Goodwin could interactive with him to gain information and give him information each time. Not forgetting designed to simulate and keep him from shock, by making him believe that he was a healthy able bodied man.

When in fact he was physically mutilated due to the helicopter crash.

The cold could have been a result of the chamber of his physical body, perhaps regulated temperature had dropped sudden, resulting in his mind playing out what his body was feeling.

It could also be a sign including the hydraulic fluid leaking, that Colter had severe brain damage, and only limited brain activities like cognitive, as shown when Goodwin asked him to put group of cards in order.

Colter wouldn't have been able to open the hatch nor see anything outside the window, as the simulation existed only inside the chamber pod.

The capsule was entirely imaginary, I believe something he himself created in his head based on the container holding his actual, physical body (hence the resemblance of the capsule window to his container window, as well as his continual complaints about the cold).

The clincher for me is the final sequence, when he chose to go on one last mission to save the train. He went from sitting in a wrecked capsule in his T-shirt to being strapped into his seat, back in his flight suit, in a single cut.

The capsule's condition is representative of his own mental state. It's damaged and leaking when he's confused and scared. It's fully operational when he's confident and clear-headed.