Good timing on this one -- I just had my car (10/09 build) coded for the Alpine upgrade today. I would say that it sounds *very* different now that it's coded-- and the gong is now correct once again.
I see that the date on those instructions are 7/11 -- my 3/10 instructions for the same kit DO say it requires coding - and my car certainly did. My CIC was replaced a few weeks ago (due to failure), so it had the most current SW on it.
Its pretty clear to my old ears that the coding removed the equalization on the HU and it seems to have made the bass a lot less 'muddy'. It now sounds 99% of the H-K system. And it only cost me $150 to get it coded.