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So it is only wasted when it is not needed after. I think it is minority of cases.
In general, I feel that proliferating on thee input (read, before assemblers) is the most sensible thing to do, especially if you are doing partial upgrades. It also aligns with the fact that you can't proliferate ores at mining point.
The only things that make sense to proliferate at production point are end products like sails/rockets/lenses
The vast majority of modules I have still set to extra products except some long recipes ike plane filters or carbon nano tubes.
https://steamcommunity.com/sharedfiles/filedetails/?id=2747857037
I tried this with red cubes and it increased production by 25%, but 25 extra red cubes every ten minutes really doesn't make a lot of difference. So I'm going to keep playing around with this mechanic but I think it will be most useful later game, producing sphere components, that sort of thing. This is what I mean by increasing spaghettification in early game.
https://steamcommunity.com/sharedfiles/filedetails/?id=2747878488
That said I didn't use it on my research cubes until I had PLS unlocked, you can dramatically reduce the spaghetti that way.
https://steamcommunity.com/sharedfiles/filedetails/?id=2747933691
Personally I find MK2 to be the sweet spot double the extra products vs MK1 and 80% the extra product of MK3 but only uses coal and has much lower power requirements.
I have all my cubes set up for 3 per second, I then proliferate the last 2 steps so I get 3.6 cubes a second and then I proliferate the cubes so I get hashes as though I had 4.32 cubes a second which is nearly 50% more hashes.
But yes it really shines with longer and more complex chains. With green cubes for example if you're using coal for the graphene needed then fully proliferating with MK2 proliferator using extra products (despite using coal) reduces total coal used, reduces total power used and reduces all raw materials needed by about 70-80% per cube.
If you're using fireice for graphene then it uses more coal to use proliferator, but only a little bit more.
But for things like carrier rockets it can reduce your factory size by a factor of two while reducing resource consumption by a factor of three.
Spending a little coal for some bonus science seemed a no-brainer.
(Didn't proliferate the production lines for those components, though; that didn't seem worth the payoff for blue or red science.