Not sure what you mean by "they are different". Sounds like he has 12 identical panels. The only difference would be that each set of six would be on a different side of the roof. With each set of 6 in series, and the 2 series strings in parallel, the side not getting as much sun should just produce less, but not reduce the output of the set producing more... I don't see the problem you are referring to.
I'm not bringing up temperature adjusted VoC only because in the scenario of only having 6 in series, his total VoC is so far below his 500V limit that it's not going to be close regardless of temperature.
I'm with you, though, that I like to run higher voltage series strings in general. However, his proposed configuration is probably the best way to be able to utilize all 12 of his panels with the single charge controller he's working with.