@AllTimeMine  
Ah, I see. That’s a bummer. Still, improvement is an improvement, so if this will let me get crafted weapons on pair with firearms, I am game.
 
If I remember correctly, Acid Spitter is like a silent shotgun. It doesn’t do any knockback and have low DPS, but I found it to be supricingly efficient (and it damage armor very quickly).
 
Buckshot is like a powerful shotgun, though while it do a lot of damage, it does struggle against armored targets.  
The final weapon from repair lv5 have impressive accuracy and decent knowkback, but it runs out of ammo quickly (pity you can’t craft ammo for it just like you can craft acid from acidic goo)
 
Considering how much ammo cost for this weapon and damage it does, I say it is more cost-efficient than expensive and weak machine guns, but it is far inferior to sniper rifles. (It takes around 5-6 shots to kill a Ghull, while sniper rifle can take it one in 1-2 shots).
 
Weapon from lv1 and lv2 though, I didn’t find it any useful. Hoofmade sword is just bad when compared to other melee weapons you find, and tiny flamethrower is just inefficient in general. (Now that I think about it, in the past when I tried to use energy weapon, I found Flamethrowers to be too weak and innacurate when compared to plasma weapons. Cerberus was just soo much better and easier to use).
 
I am not sure if upgraded version of crafted weapon can rival guns like “Remorse” and “Spitfire’s Thunder,” but I wouldn’t be surpriced if they surpass Light and medium machine guns.  
Even with perks like: Commando and Strong grip, when I tried to use light machine gun against Ghulls in Manehattan, it took me 2-3 seconds to kill one, while sniper rifle could kill it in 1 sek if it scored a crit (and damage Ghull that was behind it). I have no idea how damage calculation works in this game, but I can tell that DPS that is displayed in weapon description and DPS when you use weapon in practice are two different things. In the past I was fooled by weapon DPS and never used sniper rifles or railguns. It took an advice from a veteran for me to find out how overpowered Remorse and Spitfire’s Thunder is.

@CommanderX
 
It’s not customize just upgrade. And yes, only for crafted ones.  
I think upgrade is an alternative to the unique instances, I mean level 2 for Buckshot Gun it’s like Justice for Police shotgun.

Does this mean that we can now customize/upgrade all weapons and armors? Or do it apply only to crafted weapons? (The number of crafted weapons is very small).
 
Personally, I found crafted weapons to be very effective side-weapon. It allows me to put a lot of points into repair so I can upgrade my armor and use crafted weapons while I gather ammunition on my exploration. When my ammo to my crafted weapons runs out, I have an opening to max firearms to lv5 and start using ammo instead. While it doesn’t have as good DPS as firearms, it allows me to save gun ammo for later.
 
Still, investing into melee lv3 and getting penetrate perk is just as effective (though it doesn’t let you upgrade armor like repair does).
 
In any case, it would be a lot cooler if this upgrading option would work for all weapons and armors (especially rapid-firing ones, since they are a lot weaker than sniper rifles), but I won’t complain if it works only for crafting tools. (Only lv3,4 and 5 repair crafted weapons seem useful. Other stuff, not so much)

Finally!