Is buying from the Apple website VS Apple Store any different? I am interested in buying the new Apple MacBook Pro 15''. I wanted a somewhat personalized version though (500 GB SSD / 16 GB ram) which is not the "basic" one.

My question is this: does the Apple Store have all kinds of combinations, hence buying from the website or from the physical store is identical, or the Apple Store has only the "basic"/default configurations and if you want more (e.g 500 GB SSD vs 128 default one) you have to buy online?
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