The driver of the other vehicle couldn't see the back of your truck....maybe you need a bigger vehicle ....painted a bright colour....with flashing lights. Wait... that would describe a school bus....which obviously she didn't see that either.
If you are going to worry about whether other people see you or run into you, now isn't any different than years ago. It is up to you to pay attention to what is around you and take countermeasures and be prepared. You have to drive defensively (and also a little on the aggressive side). Be prepared for other people to do stupid things. My comment above....If they don't see the back of your truck then going bigger isn't going to make any difference.
I look at it this way...when your number is up, then it's your time. You could live in a secluded place, never go anywhere, never do anything, live in the forest miles from civilization....but then a tree could fall on you. (watch the movies "Final Destination"). I'm not going to stop riding for fear that "something" might happen. "Something" could happen driving my car to work....maybe I shouldn't go to work? Hmmmmm......not a bad idea !
Not picking on you. Just saying that I wouldn't stop riding or doing what I enjoy because of one accident that wasn't your fault. Maybe if you were on your bike you would have seen her coming and taken actions to get out of her way.
On the drivers door....impact on the back pushed the box forward, maybe bent the frame or unibody enough. Make sure you get the truck properly inspected for alignment and seriously looked at as to why the door is affected. You might be looking at getting the truck written off.