To do it this way, all weapons get the same <child entity=""/> entry as a thing.
Whether add or customize is the default behavior is handled at the component level - the Gear component in Shadowrun has this:
Code:
addbehavior="customize"
And then all gear purchase tables in Shadowrun have
The first advantage I see is better handling of ammo - check out all the ammo types available in Shadowrun, each of which alters the combat stats of the weapon - this system makes it easy to show what ammo you're using right now. The other thing that makes me wish we had this in Pathfinder is the number of modifications that can be made to normal weapons in Pathfinder - none of them were in the core rulebook, but with additional books, you can put a saw edge on the back of your sword, you can have your weapon blessed as a holy symbol, you can have the hilt made with a secret compartment and several other modifications. Also, in Pathfinder, the spell "Masterwork Transformation" allows you to take a normal weapon and turn it into a masterwork weapon, something that did not exist back when the weapon system in d20 was originally added. So now, instead of just modifying the weapon they already have to make it masterwork when that spell is cast, users have to delete and re-purchase that item.
I think it's also more intuitive to users to add a weapon and then modify it than to add a generic weapon that you then turn into a specific weapon. We get at least one bug report a week from people who don't notice the "-Custom/Magic Weapon-" item or don't realize that's what they're looking for and ask how they can create a masterwork weapon or add a material to a weapon.