"All these perks - useful in normal play - are useless if I super-stack crafting synergies."

They're not really overpowered.
Let's take my Sword and Board character than I do these "Super-Stack crafting synergies"
I wear Studded Armor, Iron Boots, Gauntlets, Helment, and Banded Iron Shield (The Iconic Dragonborn look).
Weapons are Skyforge Steel Sword, Steel Dagger, Hunting Bow, and Iron Arrows,
With use of smithing and alchemy gear and potions and the use of the Ancient Knowledge here are my character's stats.
Armor Rating: 393
Damages for weapons (Keep in mind I use heavy enchantments):
Sword: 375 Damage
Dagger: 139 Damage
Bow: 345 Damage.
I have 100 in Smithing, Enchanting, Heavy Armor and Light Armor. My Archery and One-Handed are both in the 60s. The only reason my weapons do high damage are because One-Handed and Archery are fortified to do 48% more Damage x 3 (For a total of 144% more damage).