Various arguments are as follows:
1) 3% is all the closer a slide rule was ever expected to provide accuracy, so anything tighter than that is not required.
2) We really don't know actual loadings more precisely than 3% or so.
3) CSR equation (AISC H1-1) is expressed as less than 1.0. Given normal rounding rules anything less than 1.05 would round to 1.0. (I find this rationale stupid at best, but I've heard it a number of times.)
4) Common industry practice, probably not only for the metal building industry but in general. Our certification auditors have never had a problem with the 1.03. I think Jim Fisher is comfortable with it as well and he is a widely recognized expert.
5) A number of textbooks in their examples allow slight overstresses (say OK), although I don't know that anyone has explicitly stated that 3% is okay, but 4% is not, etc.
6) Our steel will generally have higher yield and tensile values than the minimum allowables That is not a particularly good rationale for initial design, however can be of some use in litigation and failure analysis.
7) Depending on the structure, what is the range or pattern of the overstress. If it is at only one point, it is not really a problem from a practical point of view as the forces will redistribute somewhat if necessary. This is particularly true if it is at a point say for example directly over an interior column. While the mathematical model might generate an overstress, when the physical structure is examined and the depths of members and connection areas are taken into account it is unlikely that the mathematical stick model will truly represent the physical at that location. A point out at the middle of a span would be interpreted differently. If one point is 1.03, and the points 5' to either side are in the 0.80 range (as an example) it is unlikely that there will be a long-term problem. Other items like partial base fixity, bearing lengths on purlins, etc. could show that the overstress doesn't really exist if you are willing to do some heavy duty analysis and model the structure in a higher level of detail.
8) Evaluate the load combination causing the overstress, is the combination one that is likely to happen, for example 12 psf LL in a no-snow county. Pretty unlikely that the roof is going to see a uniform 12 psf over its entirety once construction is complete. On the other hand, I get real conservative in the area of a step snow drift, where there is a history of design or higher loads in actual occurrences.
Bottom line:
There is no specific allowance for using 1.03, but most everyone does it. The checker is technically within his rights to criticize a 1.029 ratio, although in general I would say he could find something better to be uncomfortable with.