There are actually two types of .50s found on U.S. fighters. One is for a normal installation and one is for a synchronized installation. The P-40B uses a synchronized installation which has a lower rate of fire than the normal version. They are still the same in a bullet per bullet comparison.
As for them using different characteristics, that's not how the system works. Lethality, rate of fire, muzzle velocity, armor penetration, etc, is not set on a plane by plane basis. There's a weapon file that is set up with all that information. None of that info is defined in any of the plane files, it just says go use this weapon for this hardpoint. These planes(with the exception of the P-40B) are all set to the same weapon.
Now this is not to say that your perception is wrong. It's just that what you attribute as the cause of your perception may be what's wrong. For example, compare the FM2 versus the P-51B. They have identical guns(I did verify all of these). Yet you note that one is much more effective than the other. What other differences are involved that may account for the disparity? Is it really that you are using different weapons or is it that you are using the same weapons in a different way or against different things?