See AWS D1.1:2008 2.16.1.1 and Figure 2.2(for cyclically loaded) and Figure 2.3(for statically loaded)..this addresses transitions between unequal thicknesses......to keep from haveing a notch(due to the sharp transition in thicknesses), you need to slope the transition between the two surfaces at 2.5 to 1.
That covers the 'How to do it' but it doesn't really answer the question.
My thoughts are that the Section 3 pre-quals do cover it but I have never dealt with that so need to look at it closer unless someone else contributes from their knowledge base.
Brent, I would place the full-pen then add additional fillets as required to get the correct slope. All pre-qualified as far as I'm concerned as long as it adheres to Clause 3 materials, filler material, processes, positions, etc...etc...
Over in one bay of our shop....I have a truss being fabricated with a WT top chord that has a 3/4" thick web(stem), bottom chord is a WT with a 1/2" stem. The stringers(back to back angles) are welded to 1/2" plates that are welded full pen to that 3/4" WT stem. The full-pen is designed to only be as good as the thinnest material(1/2") so any additional filler material is only for blending the differences in the thickness.
I guess I didn't really consider your answer properly. I thought you had just skipped the question about the Clause 3 application and had sent him to the other info. Sorry.
Should have done my followup reading before posting.