Just be very careful, when adjusting those hinges. I did not have mine aligned correctly and when I closed the hatch they bound up and stressed the mounts on the hatch side which is fiberglass. There was no way that I could fix it, and lucky for me I found a hatch at a local yard, that's the good news. The bad news is that hatch must be at least 300 lbs...
This was 15 years back, and RCs were plentiful. I check a local yard and every so often they get an RC. Every time I looked one of the RCs over,
(usually they were pretty beat up)...however I never found any with broken hatch hinges, nor any misalligned hatches. So I believe the design is pretty well made. I don't believe it is a body flex issue, seems to me there is too much over all structural metal involved in the hatch frame opening. Now if there is frame damage from a prior rear area collision, that's another possibility. Considering that these hatches are unique to that RC, which are getting hard to find with each passing year. And my experience. I would take my RC to a reputable body shop to have that hatch adjusted. I checked the online auction and saw a few RC hatches going for $400 plus. So a reasonable fee for the adjustment may be worth the investment vs guesswork.
As far as the weatherstripping is concerned. I don't think that should be much of a factor. I restored a 1964 Buick, and used Soft Seal, weatherstripping to replace the weathered OEM. The doors were a little tight to close this was 1987. However the conventional wisdom back then was to let the car bake in the sun, which in FL is not a problem.. and the seals will conform to the internal minute configuerations. After I did that the seals "set". I still have the 64 and the doors now close with no extra effort. If that is the case with this hatch I don't know. I would contact the manufacturer of the weatherstrip to get their advice.. Good Luck.