My advice is to take on board whatever @craig suggests. Unless your agreement with the installer included improving building fabric to mitigate existing cold-bridging, then you only have some minor snagging issues that you could probably have resolved yourself with some expanding foam and sealant in the time taken to craft your comprehensive and eloquent posts!
I was reluctant to pay someone to do something I could do myself; did one ceiling with a roller and realised how long it was going to take to paint the whole house... Painters are not that expensive and come with all the kit 😉
Is the 3 inches the full depth of the rafter? If so, I'd be cautious of hanging any additional weight off 75mm rafters, and be looking for a solution that added strength not just extra load I think.
Probably just tape the small bits. For anything bigger, I believe the recommended fix is to slit the membrane horizontally above the damage, slide a patch up and in so that the top of the patch is on the inside of the membrane and the bottom of the patch is on the outside to shed moisture, and then tape in place.
Once it starts, its like an expensive roller coaster ride that you can't get off until it's liveable. Pace yourself, improvise, adapt and overcome, and remember it will be worth it in the end!
I've got a 10ft container to pretty-up at some point. I think I'd drill the holes first and screw from the inside into the timber, or weld a few angle brackets on to avoid holes in the skin.
Probably not a massive oversight then; more a difference of requirements. Night latches usually require additional locks on the door for security so are superfluous with multi-point locking systems. I can't really see an overwhelming argument for having one tbh, but if you can, probably best to replace the door with another timber one and fit one.