1) Why are all buildings the same? Light switches are often in similar places and the space between the floor and ceiling is pretty standard.
2) Why are all vehicles the same? Mirrors are always in the same spots and seat belts all work the same.
3) Why are all laptops the same? Keyboard center on the bottom with a trackpad or nub near the center. Screen on top, ports and stuff on the sides.
There are components that are common in all facets of our lives that when different can cause problems or surprise which could be good or bad. We need to join two floors of a building. Use stairs! People understand stairs. We need to showcase a collection of clickable images. Use a grid! People understand link grids.
If you want to make your website usable you have to lean on expectations and those are pretty well defined nowadays. Imagine walking into a room and turning on the lights using a switch in the middle of the floor or plugging in your laptop's power cord at the top/back of the screen.
Most companies spending money on a website want them to feel fresh and creative and engaging but they also have to temper that with usability and expectations. That's why all websites "look the same" or at least why the author thinks they do.
Just because certain elements are in the same spot(s) or behave similarly doesn't mean things are the same. Or, at least, to me they aren't.