For example, is it necessary to learn 8 stances when you're only going to be using one?
Each stance has its own merit when it comes to improving the body's strength and coordination.
Sochin / fudo dachi, for example, is excellent for strengthening the legs and improving hip flexibility when practicing punches.
Neko dachi is a great way to improve single leg strength, while also improving balance.
Kokutsu dachi improves stability, while also being a platform upon which you can more easily learn how important body shifting is.
Kiba dachi teaches you proper leg tension, which is important regardless of the depth of stance.
The list goes on and on. Even if you only use a more upright, more flexibile, modified zen-kutsu dachi for kumite, the benefits of all that stance training are going to improve your techniques, strength, speed, etc.
Is it necessary to learn an archaic blocking system when more natural blocking systems have been developed?
Taking the long way is what helps you develop strength, flexibility, and dexterity. Of course you're not going to see someone making a full blocking motion in jiyu kumite, but all things otherwise equal, the individual who has practiced those full blocking motions will have a better block and a better understanding of positioning, leverage, etc., than someone who didn't practice that way.
Furthermore, someone who has trained using those full motions and has solid fundamental technique, can make small modifications to those blocks, and turn them into joint locks, throws, etc. Not only will he be able to learn these more easily, he'll also have much better control.
Is it necessary to learn deep chambered punches when you're going to be utilizing more boxing-like punches when you actually fight?
Practicing punches from a properly chambered position is a great way to develop the muscles under the armpit / shoulder, which are of critical importance when it comes to using proper bodily mechanics. Those muscles can help you with upper body stability, along with keeping your bodily alignment in the correct position, even if you're not in a chambered position.
There's much more to this than what I've described already. That's the beauty of the system, that it's straightforward, it can be learned by almost anyone willing to be patient, and it produces excellent results. Nakayama, et al., had brilliant insights into how the human body works, and those who carried on (especially Asai Sensei, even when he broke away to form the JKS) put an even heavier emphasis on developing the correct mechanics. Kata practice has always been an important part of their methods, since it is a proven way of developing those mechanics and fundamentals.
Furthermore, it's a method that allows you to continually improve, even when you're past your physical prime. I've seen first-hand, the physical prowess of Shihan Kos Yokota (one of Asai Sensei's top students), and at the age of 65, he can hit harder and faster than most people half his age.