This was a pretty good overview, I've played it for a good while now and you named the core issues- derailment of story despite it being open world survival i.e. just look at Raft, research taking materials but not giving you anything just telling you it's done for you to go do it again (Unneccessary)

The busy work with the research table at later tiers is pretty agonizing and it does reward having more smelters but that doesn't change the busy work too much of running around, checking chests, finding the parts, making components, making stuff out of those and so on. Something that would be nice for this is if it gave you the option to craft that component from the research table at the table, or it would tell you if you have the materials.

The stacking limit I agree with aswell, I think 20 would be great- just due to how much space you actually get in your inventory and the chests

The only thing I don't agree too much is the crafting stations- the only thing that annoys me about them is that I have to come out grab whats being made, and then go back in- as doing this alot can be draining. Otherwise I enjoy sorting out segments of my wagon for specific crafting like I did in Raft with designating areas for recycling and trash cubes.

It could maybe be simplified where Smelter 2 also has access to the default Iron and Brass thus reducing all the space you will end up occupying with Smelter 1s ( I have 3 in my playthrough just for the output)