Madhouse is well-known for their dedication to detail. For X-Squared and X/1999 the movie, they remade many of the sequences before they got them the way they liked. So the cels that were not used for filming are "test" cels.
All of what I call "test" cels are different from what appeared in the final broadcast, not just in detail, but in immediately recognizable color choices. Also, my "tests" are identical in the way they were painted on photocopied trace lines. Fan cels tend to have inked trace lines and in generally are more carefully executed than production cels, even what I'm calling test cels. And, I'd imagine, the fan artist would take care to choose colors that would closely match the production image, rather than differ so dramatically.
Kinda like the principle I've heard among autograph collectors: if a suspected signature exactly matches an attested genuine signature, then you've proved the suspect a forgery, since no one signs his or her name twice in exactly identical ways. The only way you could have two identical autographs is if one was forged using the other as a model. That's not what we see in test cels.