Depending on the Apple store. Most sell what they have in stock. Some have some supply of the most popular parts on hand and my be able to customize it there (I have seen some genius bars do upgrades and repairs on the spot), if you are looking for something they do not have or cannot do, they can always order it for you.
That is so not correct. Some of the Apple stores will have a pre-configured models with upgrades as well as the base models. The stores do nothing more than upgrade ram on demand, they do not install processors or GPU's, that has to be done through the online store only.