Yes, sure, more time would have been advisable. I've flown out of SAN many times and it tends to be a very efficient airport in terms of security lines, so 40 minutes would normally suffice, though it is tight. Other airports can be much slower, of course.

Once the door is closed, to answer the OP's question, it is very unlikely that it would be opened. Basically, the ground crew have closed out the flight and filed all the necessary paperwork. They'd have to reopen that and redo stuff, so even when the plan sits there for a long time, once the door is shut it's basically as if the plan is gone. We had this happen to us in FRA this summer. We were on a paid J booking and were delayed on our inbound. We cleared immigration with about 10 minutes to flight time and the gate was only a few steps from there. When we turned the corner, I saw the ground agent pull the paperwork from the printer so I knew there was no hope. We went up to the lounge and were rebooked for the next day and also received a hotel booking all while the plane sat at the gate. They had some kind of minor tech issue that needed resolving and were delayed about 45 minutes. But we couldn't get on. Such is life!