From the way you've said this, you make it sound like you expect the trader to ONLY have items for your perk tree - like finding an iron spear made all your points in agility worthless, why does it? You decided you wanted to use knives, not spears, so who cares what spear he has? It hasn't stopped you aiming to be able to craft knives.
Also if the trader only has stuff from your perks, to around the level of what you can craft, then there's zero point in traders - why would you bother with them? You'd just craft the items because it's cheaper to do that than going out of your way to quest and earn money to get decent stuff.
I've just spent the past two hours playing to day 17, in the intellect tree, and the trader has had some ok stuff, but nothing that's made me want to jump trees, I've just ignored those items because I'm focussing on the intellect style. Rewards and items are also not that amazing that I'm seeing either.
I don't see this as a big problem in the slightest, I've not been skipping parts of the game, I've been doing various bits of crafting, certain mods, some weapons, some armour etc. I've been looting for some stuff, and buying other things - I've been basing my decisions on my character, and where I can currently get the best items. Sometimes that's been crafting, other times it's been looting, other times it's been quest rewards, and other times that's been buying from the trader. I don't see that as unbalanced, as I've been doing all of it. And I still don't think I have anything really special or anywhere near end game. He's had a steel club for sale recently, but why would I pick that when I'm playing for the stun baton, and all my skills are in that?
And how do you know the magazine system is the full intended line of progression in terms of time? You are making an assumption there. What if it's exactly what I'm doing?, Where I'm using a mixture of different parts of the game, to get whatever I need/want at that particular time. I've only just got onto iron tools btw, which I think is reasonable, one I bought, one was a quest reward, and the other one I crafted.