generic rules for contradictory universes

I've been reading some of the fighters debate, hoping that 
whatever comes out is simple.

Anyway, I'm wondering whether you _can_ support 
contradictory backgrounds with generic rules.  Suppose 
setting A does a lot of damage to capital ships through 
fighters, and setting B has defenses on the big ships that 
make fighters keep away.  Can you really bounce out both 
worlds with generic rules?  If you provide for the supposition 
of setting A, aren't you violating setting B?

Or is that kind of multi-setting support not what is being 
discussed?

Side note: I do prefer simple.	Ordnance was one of the 
things I liked about BFG.  Torpedoes can attack ships.	
Fighters remove all other ordnance and are removed 
themselves (they return to carrier).  Bombers are removed 
by fighters (which go back to carrier), ignore other ordnance, 
and attack ships.  I'm not saying Full Thrust should do that, 
but I liked the simplicity and basic premise for torpedoes, 
fighters, and bombers.

thanks,
andy