MechWarrior 2: Resource Forum

I've noticed that the custom variants that come with the Netmech download tend to spread all their weapons out, generally only putting one of a type in any given location. Is there a utility to this beyond simply not having all your eggs in one basket, so to speak?

You pretty much got the reason correct.
Weapons should be spread out in the torso and head.
The less weapons in a specific location the longer you will have a weapon to fire.
One should never put weapons in the arms unless they expect to lose them later on purpose.

In MW2, all weapons, including those in the arms, fire to the front. MW3 added a feature where the arms could be flipped to fire to the side, making mechs without the ability to torso-twist a little more attractive. But as MW2 does not have this feature, there is little use in putting weapons there. Mechs that do this, like the Gargoyle, are easily unarmed and can then be ignored. Even more so since the Gargoyle does not have jump jets.