Mark,
Not sure how MUCH difference the alignment of the primary chains actually makes, but I think it does. It appears that they are "offset" in all actual photos in the shop manual excepting a drawing, Fig. 3-91. As best as I can blow them up to see, Figs 3-75, 3-76, 3-84, 3-85, 3-88, and 5-3 all look like the chains are "offset". There is no mention that I can find regarding this in the manual. I have always assembled them "lined up" like in your picture because I tend to be a symmetry kind of guy. But I had already made a decision that I would "offset" them on future builds, stock or not. Now granted I made this decision based on a performance engine I am building and was trying to leave no stone unturned. Should be applicable to a stock engine as well. It makes more sense to me to "offset" them because on an OEM chain I recently measured, there was .026"/.66mm difference in thickness between the inside and outside links. I think the "offset" will effectively "balance" the combined strength of the chains. It might reduce some of the primary noise that becomes very evident when the timing and carbs are not closely synchronized.
Frequently you will find uneven "stretch" between the 2 chains when examining a teardown of an engine with some miles on it. I have never checked the chain alignment during any previous disassembly but will note it in the future. It is my understanding the uneven stretch is cause by variation in the original chains as well as the distortion that takes place in the crankshaft, transmission shaft, primary cushion rubbers, and the cases under hard acceleration. The sprockets on the primary drive are able to move independently. It was very common back in the day to weld these sprockets together on high performance application machines but only recently have I given this much thought.
Keith