So there’s a lot of incorrectness here. First of all, Best Buy does charge $100 more if you pay full price for the phone, but this is not new, nor is it specific to the iPhone. Also, you can price match it within the return period, and if you get it on an installment plan, you’re not paying the $100 extra. You’re paying the same price as everywhere else (unless whichever phone your buying is on sale that week, in which case you’d pay less).
Secondly, Best Buy sells Universal Carrier Devices, which means Best Buy receives from Apple and sells to customers the same model of iPhone no matter which carrier you intend to activate it on. This would mean that it is the model with the Qualcomm modem, even if you purchase it on AT&T. The only time you would get an iPhone with an Intel modem is if you purchase your phone from AT&T or T-Mobile or from Apple for one of those carriers. Keep in mind that this is different than an unlocked phone. These phones will lock to the first carrier they’re activated on (with the exception of Verizon, which never locks their phones).
As far as inaccurate shipping estimates, this is largely because Apple does not tell Best Buy in advance how many iPhones they will be getting, and Best Buy doesn’t find out until after orders have been placed. You could argue that Best Buy should be more conservative with their shipping estimates, but either way it would be very difficult for them to be 100% accurate until they know exactly how many phones they’re getting for launch.