Firstly, well done for sticking with the car and even better, doing the repairs yourself. I really felt for you after the accident, all that work and then you end up back where you started. Some folks would have given up at that point, so well done.
Now, panel fit.... Well, my TC hasn't, to my knowledge, ever been hit hard. There was what looked like a car park scuff on the NS front arch when I got it but since then it's been back to fibreglass twice for resprays and I've not found evidence of any significant repairs. So let's assume it's as it came from the factory ?
Panel fit on the doors isn't bad, not as good as a modern car but pretty good for the era and probably stunning for Lotus at the time. (the Elans.... well, you wouldn't use the term "panel fit" there) But front and rear bonnet, boot is "mehhh". The front can be reasonable, I can get the hinge area ok but by the windscreen it always seems to be out at one side or another. The panel is most likely warped and I'm too lazy to do anything about it.
The rear deck was just as you describe, the panel was clearly never intended for this car and it had been like that forever.
And then in 2021 I fitted a rear deck lift and finally decided to do something about it. I adjusted the front hinges to get as neat a fit as I could, at which point the angle of the rearmost panel (where the lock is) stood proud of the bodywork and didn't follow the angle of either rear wing. I can't recall the exact measurement but guess around 0.5", that's probably the same as yours ?
I cut the hidden sides of the panel taking out a triangular wedge on both sides so that the rear panel now flexed easily. Push it where you want it to be, hold in place with gaffer tape, remove the panel and lay up new glass from the inside.
But it still sits low in the middle section, nothing really to be done about that without a lot of glass work. Personally I think it's just typical of the period, these cars were thin, hand laid fibreglass and nothing like the method used on the later cars where there was much more control.
Brian