I haven't seen the CotG Final Cut, but from what I've heard, they didn't have a HD version of the "traveling through the gate" FX sequence (from seasons 1-8), so they changed it out with the FX sequence they did have in HD: the one from seasons 9-10 and Atlantis.
As others have pointed out, that effect comes from the movie, so an HD version shouldn't be a problem. But more to the point, if the producers were so worried about finding stuff in HD for their re-edit of the pilot, why wasn't it released in HD? It's only out on DVD as far as I know.
Fox (the home video distributor for MGM) or MGM itself probably got cold feet on declining BD/DVD sales (which also killed the made for DVD movies).
What's kinda odd is that the Final Cut has apparently never aired on SkyOne or SyFy. And there are no HD rips of it available from "other sources/the Asgard" or iTunes either.