War Marchine lists look quite different due to the caster mechanic and the influence that casters have on the game. I don't think the dual list would work as well here in X-Wing and would simply hurt those who run unique pilots while doing nothing to those who favor generics..
Example:
List 1,
3x Bounty Hunters: 99 Points
List 2:
2x Bounter Hunters
1 Bounty Hunter with munitions failsafe
100 points
...would be a totally legal two lists. It's different, after all.
But if someone wanted to use Jek Porkins in both list, he couldn't. It really doesn't make much sense.
Now, if we were to ban people from using the same TYPES of ships in either list. Well, then we'd be talking!