You're starting from premises that don't make any sense - that your average peasant is going to magically bhe able to get Craft and Profession skills from nowhere, that there is an infinite amount of work for members of any particular Craft, and similar nonsense - and then you turn around and say "See? the system doesn't make sense!"
No. I'm starting from the premise of skill points. Since there is obviously a misunderstanding, I'll attempt to clarify my position.
1. A peasant has, on average, 12 skill points.
2. He therefore has 12 skill points 'worth' of skills.
3. Given that he has to use the 12 skill points, we have to ask ourselves which it is most likely that he will have skill points in. I have discussed the other possible skills that he would have them in, and it is fair to assume that he puts some skills into Craft and/or Profession.
4. Thus, he has Craft/Profession skills.
The problem is not in the assigning of the skill points, but in the assumption that there are skill points to assign. I will freely admit that the average medieval peasant did not have 'skill points': an accurate model would give him far fewer than twelve (and make him illiterate, but that's another topic). The problem is not the 'automagic' assignment of skills, but the 'automagic' having of skills (and literacy) which I believe to be inaccurate.
Of course, even if the peasant doesn't have Craft skills, then his default nets him more than five times his usual wage, even using improvised tools. Why would he not therefore do this?
Though, if this still doesn't convince you, I hold to my unassailable point that even 'skilled' professions do not get their dues in the DMG. The cook earns 1 sp, and since Profession [Cook] can't be used untrained, it is the minimum that (s)he has one skill point in it. Given a seven-day week (most likely for cooks) and taking the Profession earnings guide, the only way to vaguely reconcile the two would mean she has an average check result of between 1 and 2. Unless the typical cook has a Wisdom of 1 and is furthered cursed with a -4 to skills, taking 10 will yield more than a check result of 2.
I know that the PHB figures are 'guidelines' to PCs, but is it really right/accurate that PCs should earn manifold that of an NPC for exactly the same job. Of course not. However, since the equipment lists are presumably made in mind to the low DMG wages, the better way of reconciling the two may be to divide the Craft/Profession earnings by five. Or times the DMG wages by five, if you prefer. But clearly at the current the two are irreconcilable.