Thank you for the helpful information. I had hoped to respond to your post sooner but this issue just got resolved, (sort of).
The E.O.R. allowed the contractor to weld the anchor bolts without doing a P.Q.R. because they are A.S.T.M. F1554, grade 36 and this particular gravity column wasn't holding up much weight. The steel contractor submitted several pages of documentation including the chemical analyses of A.S.T.M. A36 steel and A.S.T.M. F1554 gr. 36 anchor bolts, (showing them to be nearly identical), and an Engineering FAQ from A.I.S.C. showing how to weld a short anchor bolt.
In the future, I think the best solution might be to do a P.Q.R. under A.W.S. D1.4 because at least it allows the Engineer to specify other materials and the welding procedure would be closer to that of rebar than of pipe, plate or box tube.
Again, thanks for your input.