I recently had a 401 nailhead built. I was prepping it for paint and noticed the rods were put in as if number 1 was on the front left bank. Number 1 is correct to the front right bank (pass side). The first rod to the front is marked #2 in the #1 hole. At TDC the cam is indexed correctly. I'm thinking rods don't care where they are as long as the caps match the rods. The complete assembly was balanced.
Maybe the builders #1, is different from your #1. You're looking at it from the firing standpoint, and he may be looking at it from an assembly standpoint. Just a thought
If that is the case his #1 is 1-3-5-7 on the drivers bank. Buick's are the same but on the passenger side. It all ends up being correct with the correct #1 being at TDC and the cam in time with that.
It really doesn't matter where the rods are installed as long as they are oriented correctly. All the rods are the same before they stamp the numbers on them.
Will be fine as long as rods are facing correct directions. Typically rods are slightly beveled on the side that would face the crank throws. More than likely someone who is more familiar with SBCs did the teardown and stamped the rods as they were taking them out. Why not call the engine builder and ask him? He might actually know what he did and why. We can only speculate here.
Cylinder #1 on a Nailhead is indeed farthest forward, on the passenger side. Your builder may not know this. Best to check and see.