There are some vehicles that come off the factory with glass that has already been darkened/tinted. These are what you call "factory tinted" glass and it's common among Sports Utility Vehicles and some trucks. Usually almost all the "factory tinted" windows that come out the manufacturer has a black shade. The problem with this type of glass is that it has limited protection against the suns heat and its damaging rays. It has also limited protection against the interior of the vehicle which could be prone to fading.
Aftermarket tint also known as window film, however is different. The term "aftermarket" refers to any add-on service or product installed after it is purchased by the owner. Aftermarket tint is the application of plastic shaded material to the windows of a vehicle. It has an adhesive layer on one side that is protected by clear plastic liner. It is often installed by professional tint applicators and it comes in different variety of shades. Window film offers safety, great heat rejection and increased comfort. It can also be applied on top of the "factory tinted" window for improved performance. The downside though, on most window films are their prone to discoloration when they get older.
In summary, "factory tinted" glass offers less protection and safety than its "aftermarket" counterpart.