I CTO'd my MacBook Air (maxed out 8GB/13inch/512GB SSD), ordered online and shipped to store for pickup there. Ordered on the evening after the WWDC keynote, Was told it would arrive in store on the 20th, but it actually shipped early and arrived on the 17th.
FWIW: Mine came in the standard box, but had cellophane plastic wrapped around it with labels that had my name on it and a special barcode to scan, so the store staff knew who that particular MBA belonged to, and that it wasn't part of the regular for-sale stock.