The only option at the Apple Retail Stores will be the base models themselves. For a MacBook Pro or iMac, you can have the RAM upgraded at the store itself. They won't have a computer with 8GB installed already, one of the Geniuses will take care of it. With the MacBook Air, the RAM is connected with the logic board so it can't be changed later.
The good news is, you can have the computer shipped to your house or shipped to the Apple Store of your choice for Personal Pickup.
That's not entirely true. A lot of the bigger stores have 8GB configurations in stock. For instance, I got my i7/8GB/256GB 11" at Grand Central, and the associate said that they had other "non-standard" configurations in stock, as well. Also, the Retina MacBook Pro also has non-upgradable RAM, so it's the same situation (for those who want 16GB RAM).