Is buying from the Apple website VS Apple Store any different?
Nope, it is not different.

On apple store you can customize:

In you case it will come up as

Configure your 15-inch MacBook Pro with Retina display

2.5GHz Quad-core Intel Core i7, Turbo Boost up to 3.7GHz
16GB 1600MHz DDR3L SDRAM
512GB PCIe-based Flash Storage
Intel Iris Pro Graphics and NVIDIA GeForce GT 750M with 2GB of GDDR5 memory
Backlit Keyboard (English) &amp; User's Guide