I think one thing you need to look at when examining any engine is how it stores it's data structures. Many FPS engines use a BSP tree type structure since most FPS play areas are neatly sectioned rooms. However, while you might be able to use such structures for a flight sim engine, it wouldn't be optimal by any means.
As always, there are millions of solutions to any one coding problem, but only a few optimal solutions. When it comes to a 3D engine, you have to tailor your engine to match your problem for the most part. Someday we may have enough slack processing such that we can brute force any solution, but today you still need to look for the best fit.
flf