Seems to miss a lot of the important cities, too.

As has been pointed out (frequently), the Egyptians really weren't into astronomy/astrology. Placing cities/monuments in accordance with "signs in the sky" is usually a very, very bad idea. You never know when that next (supposed) "sacred point" is going to end up smack in the middle of a quicksand pit or in an area that gets inundated with every heavy rain. And if you missed the "sacred point", well, gosh, wouldn't the gods be mad at you for not being accurate?

I don't see it, frankly. They built where it was most convenient, just as we do nowadays. We don't place military forts or scientific companies or even towns in places where "it matches the design of that pretty constellation!"