No set pieces were created for the cockpits. As with everything else, the are CGI.
The actors sat on a moving prop element nicknamed the "Rig." It was a blue platform mounted on a large truck inner tube. Four operators (grips) manned the Rig, rocking to and fro on cue from the Director. The actors then had realisting flying movements.
The CGI cockpits were matched digitally afterwards.
The Stormtrooper armors, weapons, helmets and suits (and possibly Vader's costume), worn by the actors, were not made for the game, but are the actual props seen in the original movies, taken from the archive storage of Lucasfilm.
The rest is CGI
From Lucasarts' official site:
To direct the video, the Rebel II team recruited veteran filmmaker Hal Barwood. Now a Project Leader at the LucasArts, Hal was responsible for Indiana Jones and the Fate of Atlantis, Big Sky Trooper, and Indiana Jones and his Desktop Adventures. Before building in cyberspace, however, Hal worked in Hollywood for more than 20 years. He co-wrote Steven Spielberg's first feature film Sugarland Express, and produced and co-wrote the films Corvette Summer and Dragonslayer. His unique combined knowledge of both the film computer mediums made him the ideal choice for the job.
Enter your pilot name as any of the following to activate an outtake:
"Gary Martinez" - Outtake with Gary (Admiral Sarn) and Darth Vader
"Jamison Jones" - Outtake with Jamison (Rookie One) during briefing
"Julie Eccles" - Outtake with Julie (Ru Murleen) and strormtrooper uniform
Press and hold Alt + V in the main menu the game will ask you for an activation code Type 'quotovres' and you'll enter theater mode ... in theater mode you'll see shadows of Darth Vader and R2D2 throughout all the cutscenes ... moreover there's a whole NEW dialogue going on there - the speech is turned off and all the subtitles for the cut scenes are changed... the new subtitles are much, MUCH funnier and they also include some cool Star Wars jokes...
The cloaked TIE Fighters appeared in "X-Wing Alliance" as well. The Super Star Destroyer "Terror" has been referred to in some books and comic books, and its mysterious mission and purpose slightly alluded to.
According to Lucasarts' old quarterly magazine "The Adventurer", "Rebel Assault II: The Hidden Empire" was the first media since "Return of the Jedi" to incorporate live-action actors and footage in the Star Wars universe. Apparently the editors of "The Adventurer" didn't feel that the "Ewok" movies did not count (and by all means they don't, since none of those movies really reference to anything in Star Wars except Ewoks).
Jamison Jones, the guy who plays the main character Rookie One, also played "Booth Gunderson" in the episode "The Easter Bunny" of Beverly Hills, 90210. He also played "Edward Proxy" in the episode "People v. Gunny" of JAG.
Julie Eccles, the woman who plays Ru Murleen, can be seen on Indiana Jones and the Last Crusade. She plays Irene, Indy's secretary.
Rebel Assault II is the first LucasArts game that used INSANE, a proprietary animation engine. INSANE (Interactive Streaming Animation Engine) greatly compresses moving images so that high quality full-screen videos can be displayed even in hi-res graphics modes on the PC.
INSANE was later used in other LucasArts titles such as Full Throttle, The Dig, and the Curse of Monkey Island.
There are a lot of (I mean a lot!) easter-eggs in Rebel Assault II. For a very comprehensive list of all the secrets visit Brad Pack's Ultimate Rebel Assault 2 Home Page.