Your point? Any of this can be done and quite easily. What's the assumption you're not including here... that each of the encounters be "level appropriate" in some way? Is that what you think the "hard part" is? Why would we try to balance these encounters around some kind of combat model other than allowing the NPCs to be the threats they naturally represent?
I'm about to quibble here. I apologize.
For two of them I agree, 3.x handles it just fine. But the blacksmith example is one that always tested my suspension of disbelief. In 3.x, max skill ranks are based on level. So to make a blacksmith of truly legendary ability, you'll need to level him up. You're probably using the expert class for this.
A 10th level expert fits the bill. Let's ignore any advantages he might get out of superior equipment and circumstantial modifiers. His bonus will be 13(skill points)+3(ability mod)+3(skill focus)=+19. Not bad. Hits DC 29 on an average roll, which is pretty legendary. He also hits DC 20 on a natural 1, which is the DC for masterwork equipment.
The problem is that he's only supposed to be a blacksmith. He's not a warrior. But because we raised him to 10th level (the only way to get his skill bonus high enough), his hp, attack bonuses, and saves are going to be beastly. especially using some of the masterwork equipment that he can easily make. With a con mod of just +1 (I think a blacksmith of such skill should have at least an above average constitution) his hp is 45 (10d6+10). His attack bonus with a mace is +7/+2, without a str mod (he probably has an ok one).
He can take on low level characters pretty handily, which may not be what I was looking for. Maybe I just wanted him to be a craftsman with no real combat ability. The disconnect is even more obvious when we choose a profession that isn't necessarily physical, like a legendary silk weaver. Why is the best silk weaver in the land able to make iterative attacks?
You ask "Why would we try to balance these encounters around some kind of combat model other than allowing the NPCs to be the threats they naturally represent?" In this case 3.x is modeling our silk weaver as something other than they threat I think they should naturally represent, but I don't have any choice because of the way the skill system works.
But hey, any system will have brainfarts like this. Like I said, this post is a quibble. It just happens to be something that bothered me quite a bit back when I was GMing 3.x as a young lad. These days I'd just stat up a level 3 expert real quick and give him a +10 "awesome at silk and stuff" bonus to his craft check and call it a day.