In no particular order...
It seems a lot of people studying this case try to come to absolute conclusions about things that can not be definitively known. Sure one must speculate possibilities and likelihoods, but...
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Reserve containers - R99 confirms that some of those containers used cones rather than closing loops. That complicates re-closing the container. As I remember, the holes in those cones weren't very big, might be difficult or impossible to thread lines through them to tie the container shut. If the real one had cones and the dummy had closing loops, that would be a reason to switch. I would guess that they would use closing loops on the dummy for ease of repacking. Yes, pilot chutes have springs, but no, those reserves would not have pilot chutes, as they used the hand-deploy method of reserve deployment. If half the canopy was removed on the dummy, it would indeed be softer when packed as there is less bulk/density in it. My guess, though, would be that if he used the container he might have removed the canopy. If he left that on the plane, it could easily have been blown out the door at any time.
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The 'pressure bump' on exit - Eric has the right idea about that. The pilots would not feel simply the weight loss of Cooper jumping. Even the largest commonly used jump planes, DC-3's then and Twin Otters now, are much smaller and less powerful than that jet, and you just do not feel it when people exit. Go to a drop zone and take an observer ride. It's not like you're sitting on the edge of a springboard when someone launches a triple-lindy off of it. Rather, what they felt was the recoil of the stairs. Look at the size of the flight control surfaces on that jet, look at the size of the trim tabs on those surfaces. Then compare the size of those stairs. When Cooper's weight caused them to lower as he climbed down them, the pilots should feel that, then when he goes, that weight is suddenly gone and they recoil in the wind, that's what the pilots felt. That would be the same whether he jumped or pulled off the stairs.
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Pulling off of the stairs vs. jumping - I personally wouldn't like that idea, but I'm experienced and know the problems that might cause. But other people, including 377, have suggested that possibility and that may be what Cooper did. I wrote a more detailed piece about that on dropzone the other day. I also wrote a piece there about 'dangling' the load vs. tying it on securely.
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Jumping with stuff attached - First, I don't think that a spinning, tumbling, out-of-control freefall necessarily results in a no-pull. If Cooper's got the nerve to pull off the hijacking, I'm guessing that he has the presence of mind to pull. One puts the rig on and familiarizes one's self where the ripcord handle is. However out of control one may be, the handle is still in the same spot. I've seen people pull in some pretty f-ed up positions, and they get open. - I think all smoke jumps, and many military jumps with loads are static-line, so no freefall issues there. But many military 'loaded' jumps are freefall. And look at modern sport tandem jumps. We jump with people(!) attached to us. A lot of them are 230lb beer-drinking lunkheads. Many of them do not perform to their training. Some of them are downright uncooperative, kicking, flailing, going fetal or 'catman'. And we pull it off, it's not that hard. But yes, we're experienced and know how to handle it. Freefall stability really isn't that hard, but it can be subtly tricky to learn. It's kind of like learning to ride a bicycle - it can be difficult and wobbly at first, but once one 'gets' it, it's pretty intuitive. So if Cooper is experienced, it's fairly easy. If he's not, well like anything, some people take to it easier than others, so it may or may not be a problem. My educated guess is that it's way more likely than not that Cooper survives the jump. Whether he's injured on landing, and that hampers his egress, that's another issue...