"My favorites are the first two movies, so I want to make a film that's connected to Alien and Aliens. That's my goal. I'm not trying to undo Alien 3 and Alien Resurrection, I just want it to be connected to Alien 1 and 2."
That's not a denial; it's an evasion.
Superman Returns didn't "undo" the later Reeves movies either; it ignored them. Note that even the question of when Lois became pregnant isn't addressed unambiguously - one is free to assume that it was during the scene in the Fortress in
Superman II, but if one wants to place it later one can.
With regards to Superman Returns . . . exactly. For all we know, that version of Superman
did run into Richard Pryor at some point or battle Nuclear Man, but there was simply no reason to mention those particular adventures years later. Returns wisely avoided mentioning those movies, but that doesn't mean they were "officially" stricken from the continuity--whatever that means.
In general, the internet tends to worry more about what's "canon" and not than the average moviegoer or even the filmmakers. Ninety percent of the time, there's no reason to formally "de-canonize" something; you just quietly agree not to talk about it anymore.
As for going backwards . . . PLANET OF THE APES provides a useful example. When the Tim Burton remake failed to catch fire, Fox did
not decide to to back to the original continuity and pick up where BATTLE left off. Instead they simply rebooted the franchise a second time.
Which is what will likely happen with Trek. If and when the current cycle of movies runs it courses, we're more likely to see
another reboot than a new series picking up where VOYAGER left off.