A very interesting discussion.
It looks to me like there are three separate questions that get combined, although they don't have the same answers.
1) Will it fail?
2) If it somehow failed, would I be considered negligent in a court of law?
3) Does it meet the code?
Now, it seems that everyone agrees pretty much on #1. That a 3% or 5% increase, by itself, with current codes, isn't going to cause a failure. And this seems to be the point that the Wooten article is getting at.
Question #2 seems murkier, with conflicting opinions given above.
Question #3 seems to me to be the sticker point, though. When you have a set of drawings that purports to meet a particular code, and seal those drawings, are you certifying ONLY that the item will not fail?
Let me give you an example from my field. In pressure vessel codes, you might have an equation given for wall thickness along the lines of t=PR/S, with P, R, and S being pressure, radius, and allowable stress. But the exact equation to be used will be specified. And somewhere in that same code, you'll find tolerances for allowable plate underrun. So when you calculate the thickness as 0.52", can you use 1/2" plate? Generally, not.
Now, if you look at the failure of that 0.52" plate, you'll find that they recently changed the code safety factor from 4 to 3.5, and that other codes use different safety factors where perhaps that same plate could be 3/8" plate. So the issue of it failing for lack of that 0.02" is pretty much a non-issue. But the question of whether you've met the code still remains.
Switch from this to say, a building, where you have very involved loads and analysis, and could approach it quite a few different ways. Suppose you calculate the beam stress as 25,000 psi and the code calls out 23,760 psi maximum. Can you say you met the code requirement simply because the problem got more complicated? Or that you meet the code because the loads are more approximate? Or that you meet the code because the code failed to specify a tolerance, or specified it in an ambiguous manner? Maybe you suppose that you could go back and re-work your loads and analysis to make the numbers work, but you haven't actually done so, either. What then?