Unlike many other guitar models, for Fender guitars the easiest part of the manufacturing process is almost definitely final assembly. For example, a Gibson USA Les Paul has a complicated glued-in neck join (called a "set neck"), whereas Fender necks simply bolt on with four bolts. If you have the right cut for the neck and the neck pocket in the body, and the right size four bolts and neck plate, anyone could bolt on a Fender neck.
This also makes a lot of Fender parts interchangeable. In most cases, a Telecaster neck won't go on a Stratocaster body, but the vast majority of Strat necks and bodies have identical shapes, meaning any Strat neck can be bolted to any Strat body. The same goes for the pick guard/electronics assembly (excepting different pickup configurations) and so on.
Just one component can have several different qualities. Necks are a great example. Fender makes necks with different combinations of neck and fingerboard wood, different neck profiles (the shape of the back), different fingerboard radii, fret size and construction, inlay type, and so on. When you take into account all the different necks, bodies, electronics, and hardware types that can all be mixed and matched, there are thousands and thousands of combinations, each one a different type of Strat. Maybe the differences are too subtle to notice for most people, but they exist and that opens up a marketing opportunity for Fender.
The FSR thing is a deal between Fender and different resellers. Lets use Guitar Center as an easy example. Fender and Guitar Center pick out a combination of Strat components from the thousands of possible combinations that Guitar Center thinks people will want to buy and Fender doesn't think everyone will want to buy and they agree that the combination they have picked will only be sold through Guitar Center stores. That means if you want one, you have to go to Guitar Center. I'm not sure what Fender gets out of the deal but maybe GC pays them money up front or Fender can test strange products this way and see if they are popular. GC is hoping to boost foot traffic in their stores by getting people to come in and play and maybe buy a guitar that can only be seen in their stores.
It looks like at some point an FSR model will released to more vendors after a while or the exclusivity isn't 100%, since the FSR American Standard V-neck for example is clearly meant for Sweetwater Sound but is available other places (although not at Guitar Center).
To see what exactly is different about a particular Fender model on their web site, look for the "Specs" button. You can also filter by Series, Woods, Orientation, Neck Shape, Pickup Type, and Price. A better way to scope out the Fender product line is to go to a store and play a bunch of them. You'll never know if you like the V, C, or U neck profile best until you try them. (just one example)