As someone who has done bodywork for several years, here's my opinion-
I've never had a panel that I couldn't make fit. Almost all of them are going to take some finessing, but they will fit. Honestly, I've had some factory panels fit worse than reproduction panels, especially on GM vehicles. Most body on frame vehicles are really easy to get panels adjusted to fit, as there are usually a ton of different ways to adjust the panel gaps. Shims are your friend.
The biggest issue I've had with aftermarket panels is the thickness/weight of the panels. A lot of the times, replacement doors, fenders, tailgates etc. are made of much thinner metal than the original panels, so they will dent much more easily than the original panels. So on panels like tailgates that take a lot of abuse, I try to stick with factory panels.
Also, I've found that the reproduction panels tend to be much more rust resistant than the factory panels. I believe it's because they are usually e-coated really well inside and out, unlike a lot of factory panels sometimes.
Lastly, I've found that the "CAPA/NSF Certified", is usually a bunch of crap. The CAPA panels are usually manufactured side-by-side with the regular panels, and the only difference is the sticker on them. Not worth paying extra for IMO. I am legally required to minimally use CAPA panels for insurance jobs, so I use them, but I think it's a bunch of BS. I don't bother using CAPA on my own vehicles.