I agree it's mildly confusing, but this is probably not the right solution, either. CTO options are an exclusive "you can only get this at Apple.com" thing. But in this case, you most certainly can get the 2.9MHz i5/8GB RAM/512GB Flash configuration off the shelf at the Apple Retail Stores and from independent retailers. If something's available off the shelf, it shouldn't be a CTO option.
If you look at the two 13-inch MBAs, you see the same thing. There's a 128GB model where you can only CTO the graphics, and the 256GB model where you can CTO both graphics and storage.
If you analyze the options for the various iMac base models, same idea, but different implementation. In the case of the non-Retina 21.5" iMacs, both the CPU and graphics chips are different, while you have the same storage CTO options for both.
Wherever I look, the same thing - you can't apply CTO options on one base model to create a configuration that's available on another model (either off-the-shelf, or CTO) - something has to be different.
It almost seems like a rule Steve would have come up with. ;-)