If you start the movie from the Computers app on Apple TV to access your iTunes Library, then Extras may not show. Extras (if available) should show when viewing on iTunes on a Mac, or when viewing through the Movies app on Apple TV, or on an iOS device.
Extras are not available to rental titles. Extras may not be available for download. Extras availability may be be different per region of iTunes Store.
The 90 days has to do with eligibility for refunds, and undoing purchases. After 90 days you can still report issues with long term services that are not available to you at this time, just not in the legal/financial way.
However, streaming services availability is subject to change, and some titles have disappeared temporarily in the past.
Alien 3 with Extras appears in my local iTunes Store as available, though.