Good point. This is true for fertilizer, backpack and generally recipes (although you could buy/find instead of craft)I'm hesitant to say this (because I want to try out the new perk system) but I remain skeptical.
The reason is simple: I want more interaction with the world not less. I would rather scavange/craft/build something then just spend a perk point.
But for your other examples perks are just a parrallel method or still need interaction with the world as second requirement:
With armor you still need to find the armour, perks just reduce the penalties or offer an alternative
With clothing the perk is an alternative/boost and probably not sufficient on its own (judging by MMs words)
Food seems to provide immunities as well as the perks, again a parallel method. Make enough food and you don't need the perk
I'm just guessing, but probably the better medicine will still need a chem station as second requirement.