Balance reasons maybe? I don't know.
I very much suspect that is the reason.
Or more to the point, alleviating the "definitive ultimate version" of a weapon.
Ie, getting Maria doesn't necessarily invalidate the fully modded 9mm --- yes it does more damage, but the scope and extra ammo capacity of the modded weapon leave a certain nitch for it to fill still. Just like morally ambiguous choices and/or quests that have more than one viable choice resulting in differing outcomes - such that it is all about trade-offs and weighing the pros and cons.
Making it this way adds more variety and spice to the game IMO, despite the fact that it doesn't feed the eternal desire for "more, more, MORE!"

- DU