That’s because none of those are reasons for their existence. That’s just a laundry list of things that bother you, but if you want to reason about these things, you have to look at the bigger picture, at how everything fits in the game.
There are many aspects of gameplay that these intermediate products affect. For example, there’s an ongoing discussion about the balance involved in crafting building pieces. A T3 foundation requires, among other things, 15 hardened bricks, which takes 6 minutes and 15 seconds to craft, in total. Changing this would drastically affect the PVP raid dynamics.
Another important aspect is precisely the space management inside your base. There are important choices to make about what tradeoffs you prefer. Do you want to spend more space but have the benefits of T3 benches (and which ones do you prefer)? Or do you want to keep your footprint low and work with T2 benches? Again, the footprint of your base is even more important on PVP servers.
Then there’s the topic of balancing of the game’s economy – not in terms of trading between players, but in terms of the relative value (in gameplay terms) of different resources and materials. I still remember when stone consolidant required ichor and twine instead of resin and fiber. The priorities for farming were different back then than they are now, and that’s something that has a powerful impact on shaping the typical game session.
Last, but not least, consider the progression. When it comes to sandbox games, the best way to teach new players how to play is by giving them goals to aspire to. Journey steps are one piece of that puzzle, but those are just visual representation of those goals, and they can’t exist without those goals existing in the first place. Having players progress from one tier of crafting to the next is a great way to teach them about the gameplay mechanics and to motivate them to explore the world and engage with the content. You might not care about progression as much, but it’s very important to those who prefer to play in single-player mode.
In conclusion, I agree with @Tuffman: this is par for the course in a survival game, and it’s what makes the game richer.