In the early days of factory keyless entry systems, the packages were optional on many vehicles. In those days, it was a no-brainer to get an aftermarket alarm system instead. For about the same cost, one could get many more features.
Aftermarket alarm systems still have more features. After all, they are a consumer electronics product. Aftermarket alarm system manufacturers always want the latest bells and whistles to lure customers. Even if there are no new features, alarm systems are updated regularly and given new model numbers so that the product does not go stale. As with cell phones, some consumers will buy a new alarm system to have the latest nifty technology even when they already have a perfectly good, working system in their vehicle.
But factory keyless entry systems are now standard equipment on nearly all vehicles. So, consumers do not need an aftermarket alarm system to get the basic lock and unlock features. (Remote engine start is still optional equipment on many makes.) The two problems with new technology in vehicles is that (1) automakers overcharge for it and (2) vehicle manufacturers are more concerned about locking car buyers into using their dealer channel for all repairs than they are in providing durable, useful technology with a low lifetime cost of ownership. Dealers can charge whatever they want to charge for repairs because technology is making it impossible for independent mechanics to do anything except the most rudimentary service jobs on vehicles.
Aftermarket alarm system remotes are always programmable by the user, so you will not be forced to pay a hefty additional service charge if you lose a remote and have to replace it. Many recent factory keyless entry systems require dealer programming for a new remote. There is no security reason for this. It is purely the automotive vehicle manufacturers sticking it to consumers and protecting their dealers’ revenue stream.