Over on the DF21 forum, I found a great post with a link to a post mortem about Shadows of the Empire. It's just loaded with interesting info about the development of the game.
Really was a bleeding edge showcase of N64. They had a ton of problems to deal with. And it's interesting to read about how their decision to make so much variety in the gameplay lead to the need to make basically a bunch of different game engines for one game. So I guess that means that SotE is unique from DF and JK. Not much in the way of engine tech sharing, unless JK uses a refined version of SotE's shooter engine (doesn't really feel that way.)