I ran into this too... remember that the quarter panels can also be adjusted... you just have to (also) remove the taillights and the body to chassis screws and the whole thing can slide left or right to give a little bit of better alignment to the decklid when it's skewed. You can adjust the decklid while adjusting the quarter panels (slide it over slightly... you have about a 1/4" adjustment you can make there).
That way, when you properly adjust the decklid (to the frame / equidistant from the window), you can then adjust the rear quarter panels slightly to account for it if you've got uneven gaps on the sides. You do need to fix the depth though... because you can't really bring the quarter panels forward... but the whole thing can adjust 1/4" to the right or left, which can and does help align the edges.
On my daughter's 85 Fiero, we ended up having to put a 1/8th" shim in the top bolt location of the hinge mount against the firewall. It's the same shim that you would use if you were aligning body panels on say, an old school TransAm or Camaro.
EDIT: This whole thread gives me stress, haha... even looking at a Fiero decklid hinge makes me question wanting to stay in the car hobby... haha...
[This message has been edited by 82-T/A [At Work] (edited 05-21-2025).]