Is the version of Independence Day that's currently available on Netflix Watch Instantly the RiffTrax-compatible theatrical version or the extended version?
 Never mind. I've found the answer. Even though the description on my Roku box says that the movie is 2:33, the file that actually plays is only 2:24, so it appears to be the theatrical version.
[edit 2] Just got finished watching it. The Netflix streaming version works fine with the RiffTrax.