I watched the F4 rifftrax with the Canadian DVD, and it works pretty much up until the planetarium scene. I didn't know there were different cuts of the film so it kinda threw me off when Mike's and Kevin's riffs started to make no sense whatsoever . The film has to be resynced during the next scene, which is Ben and Victor in the cafe that starts with Ben burping.
There also seems to be a major sync issue during the final battle. I'm guessing the American DVD had an additional 30 seconds or so that doesn't appear in the Canadian version. The proposal scene is also edited differently. Mike and Kevin seem to be annoyed by Reed kneeling twice. That doesn't happen in the Canadian version. It also seems like the rifftrax ends rather early. Usually, they end as the credits start to roll, but this one seems to end during the last scene, featuring Victor being sealed into a crate aboard a ship bound for Latveria. Is that scene missing from the US version? If not, the boat scene that preceeds it must be longer in the Canadian cut.
I realize that they probably don't have a large number of Canadian fans, as MST3K never actually aired in Canada (except for the syndicated 1 hour version), but it might not be a bad idea to put a warning on that rifftrax, just to let Canadians know about this issue. It's probable that the Canadian version of the new Extended DVD has the US cut as the "original theatrical version", but most Canadians will probably buy or rent the original DVD.