I really like the Charts. When i first started with MKS i had trouble getting the idea behind the industries, but visualizing it helped me a great deal.
Though you should be trying to bring things in their own Industry closer together, and visualize that there is a reason behind their placement.
For example in Link 2, remove Ore-Fuel completely and bring Substrate/Metallic Ore/Minerals and their Product in their own Bubble. Same goes for Rare Metals/Exotic Minerals/Silicats. Also have multiple steps for final product. Material Kits have their use, but also can be turned into Machinery.
I haven't played around with the new stuff from Link 3 yet, so I don't know their actual use, but in your Graph, its not very clear what is mined, refined or consumable. I recommend making distinct Rows for Resource, Refined, Product and Final Product. Also don't shy away from using duplicates in the graph. Rather make production lines clearer then trying to link one resource to all things it can be used for.