Paul, it is not as "clearly" as you make it sound.i think that clearly adding the additional electrode to the first ground rod does not make a multiple rod electrode but it does complete a grounding electrode system in this case. The problem is that I can see where it gets screwy in that clearly the sole connection to the first electrode (the first rod ) is not required to be larger than the 6 AWG. The problem starts when it says size the bonding jumper per 250.66 and the table gets used and so it becomes a situation where the bonding jumper from rod 1 to rod 2 is no longer a GEC . In this case I can see where someone can argue that the bonding jumper run to the second electrode cant use 250.66(A) and could lead to a larger bonding jumper.
However, I don't think this is the intent as I am quite sure lightning could careless but alas I am not engineer.
Regarding highlighted portion of your comment, 250.66(A) applies to the portion of a GEC that is the sole connection to the rpp-type electrode. You are viewing the connection to the first rod as the sole "GEC" connection, completely disregarding the bonding jumper connection to the first rod. There are "clearly" two grounding electrode system connections to this rod electrode. Elaborating on your viewpoint, explain to me how you would ever have an other than sole "GEC" connection to any electrode. The only way I can think of is to connect the same GEC to the same electrode twice (or more )... and it's neither required under any circumstance nor does anyone do it, and I certainly cannot fathom any reason for doing so.