how long does it take to custom a new MacBook Air in-store?

The answer is no. Stores only carry standard models. Stores do not have the capacity to CTO (configure to order) in house. If you want different amounts of RAM or Storage this must be ordered. Of course you can have the CTO Mac delivered to your local Apple store for pickup but you cannot walk into a store and custom order to be put together while you wait.

As far as I know, they only sel basic models in store. Any custom order is done in manyfacturing and we, as other users, would have no idea how long it will take Apple to make yours.

If you are interested in purchasing a new MacBook Air, they cannot be upgraded for either RAM or storage at an Apple Store from inventory. As babowa has already mentioned, they would have to be factory ordered in the configuration you require.

I'm pretty sure if you contact either the Apple Store near you, or get with Apple Support, they will tell you the same thing. As such the quickest way to get one, in the configuration you want, is to order one directly from Apple.

I would ask one of the sales specialists in the online Apple store - be specific about where you want to purchase or pick up. They'd know better than support. Another way is to go to the online store and start a shopping cart with the custom stuff you want and see if you can get an approximate date before you click on finalizing the order.