The reason I ask "what else" is because it's being implied that HTV is doing a better job at X-FILES than they did with TNG, and what we're seeing at this moment is just non-f/x shots that look as good as what we saw on TNG's non-f/x shots. Because of that, I'm wondering if all the footage was messed up on TNG aside from the f/x work.
I do think it's a shame that the f/x shots were not handled to the standard that CBS has shown with the first season, but other than that I love seeing all that footage (non-f/x) newly scanned with all the detail and color. "The Measure of a Man" may have a bad bluescreen composite shot, but that's such a small part of the whole episode that I'm able to enjoy it overall.
EDIT: And I'll be honest in saying I never noticed that they used the incorrect angle footage on that episode, guess I'm just not that observant!