I've seen that page but I don't think it takes the whole production chain into account?
It's only looking at one machine. The whole chain doesn't really matter.
Obviously it adds up eventually placing them everywhere, but think of it like this: it requires hundreds of modules to do all of your furnaces that way and get +40% resources, but just mining 40% more isn't that hard and its easy to just throw down another furnace line and merge it in. On the other hand with a fraction of that many modules you could get 40% more of all your sciences, all your green/red/blue circuits, and your gears, and get 40% more out of your labs. That's not only more things being added but they do compound multiplicatively so that, assuming most of your materials are going into science, you're saving far more on iron and copper than you would investing in smelters.