With film processing, and different re-mastered editions and releases of an anime, I would say there can be a lot of differences between the image of a cel and a matching screen capture. There are differences even between multiple images taken of the same cel, depending on the equipment used i.e., scanner, camera, lighting, slight bending due to scanner size, an image shot at an angle to reduce glare, and the diverse drivers, image programs, or if an image of a large cel is pieced together from multiple scans, etc. While it is interesting to see a cel in its original context, and it could be noticed if something was really mismatching, it's limited as a means of authentication.
As an example, below you can see a setup of a fountain head from Angel's Egg. The first image is from the seller, the next two are a photo I took of the cel and a scan I made of the cel, the two images after that are from two different YouTube videos, and the last two are the same video shown on two different video players.
http://chriscelsite.rubberslug.com/gall ... mID=379940
In this case, when I directly look at the harmony cel and background in person, it has variations of aqua blue and green coloring, not well reproduced in any of the screen caps, the closest color depth and saturation lies somewhere between my photo and scan, and it has much more line work than can be seen in any of the image reproductions.
Though they're not as plentiful as some shows, Evangelion cels aren't impossible to find now. They're still a bit rich for my blood, but I've a couple of EVA-01s. I hope most of the production cels that are sold now are the real production cels. However, it is true that in the late 90s and early 2000s, when Evangelion was newer, and cels from it were impossible to find (and I was told that Gainax Studio was contacting the few who had them, insisting they pull them off their websites!), Gainax made small numbers of "official reproduction cels" that were only sold at events. They were made from the production drawings, and used the exact same materials (likely even the same people) that were used to make the production cels. They were expensive, priced between $300 and $500, and were even advertised as being indistinguishable from the real cels used in production! I know there was an awesome vertical pan one of EVA-01 that I didn't have the money for, when it showed up on the secondary market. I can't even find a picture of it now; and I don't know how many other “official reproduction” cels they made. At about the same time, Cellu-Club also made both handpainted and printed Evangelion reproduction cels, although images of their cels are easily found online.