Please, I just went through a full episode of withdrawal symptoms


Yes, this is a very fun 'game' (or factory simulation editor) to play..
I haven't got a clear graphical picture of everything what you shared, but are you playing with some kind of cityblocks layout?
Personally I view trains as a similar system as anything else in the game. Things can backpressure and that's OK. But there does need to be enough space for this backpressure to go. For example with oil, in earlier game versions it was by the far the most scarce resource in the end game. Each pump degraded from 10-15 oil/s to just 0.1 oil/s. At later stages you could have the energy to boost them, but still, even with a 500% boost its only 0.5 oil/s
So the design requirement is: this pump must never stop operating. How frequent do I collect oil packets to send out to base? How much capacity is being used there? How much do I want to store for bursty moments? Those then are basically also consumer/producers in a very isolated form, and you can easily calculate the required buffer size.
I did a similar thing with trains. Just build a stacker that can hold as many trains needed. But in city blocks that is obviosuly harder. However, I did see there is a logistic train mods that only sends out trains "on demand", and will reuse trains for different routes. That seems a lot more managable.
At one point I also looking into mapping Factorio onto dataflow graphs. However, with the recent addition of Quality in the Space Age DLC, this wasn't so easy anymore. I wanted to calculate the ideal ratio of productivity : quality modules in each machine. The wiki had some information on this using Stochastic Matrices:
https://wiki.factorio.com/QualityHowever, these matrices make a few assumptions. For example, they assume that you want to go from [Plain Resource] to [Legendary Product] in 1 machine step. Whatever is left gets recycled at 25% return (and crucially: a quality bump). Its not too hard to derive solutions that converge within just a few matrix multiplications.
Then the "meta" became to introduce LDS shuffle, space bingo, and a few others.. and basically crafting legendary 'everything' became almost trivial. Once you have all legendary resources, you don't have to think about quality anymore.. you just shifted a regular factory to legendary and almost everything gets a 150% bonus.
I read in 2.1 that they removed space bingo. So that makes it a bit harder again, which prompts for some research I was doing just when Space Age came out. I wanted to see if I can optimize my factory when I don't just keep recycling intermediate products to get to legendary straight away. Why don't I do like Smelt Iron => Craft Electronic Circuit => Craft Advanced Circuit => Craft Processing Unit
And then find the most efficient way to recycle Processing Units so that I maximize its legendary output, which means I can either put a recycle loop at Iron and then build only a Legendary Factory. Or I could put the recycle loop anywhere else along the chain and try to optimize for every single production step. Here we potentially have 3-4 production steps, 3 recycling steps, and also vary the modules for every quality level, as factories for each quality level need to be built.
Unfortunately this means a design problem with 4 producers across 5 recipe quality levels, with module configurations that can hold up to 5 modules (lets say an Electromagnetic Plant), which means I have 5^(4x5) = 95 367 431 640 625 multiple configurations to simulate. Ouch! So I was looking at another way of how you can design factories with a certain "item quality distribution" (much like we have a probability density function in statistics) and then find the optimal module configuration for the next "item quality distribution".
However, with my limited mathematical creativity to fit this onto a formal problem, I did find there is another design freedom in this "optimisation": you could prioritise which resource is recycled more or less... So even I can find a way to curtail 95T solutions, I also need some method to qualify which one is the best. Do I optimize for iron:product conversion ratio? Or copper:product? Or oil:product?
The quality system made Factorio a surprisingly interesting game. The meta is to just establish legendary resources and craft everything from there.. but building these more 'natural' factories and finding ways to model, balance and optimise them is quite challenging. I don't think I've seen anything like it in other games, as there you often don't have any sophisticated calculations beyond a single consumer-producer number, determine some logistic transporting interval, and calculate your required buffers from there.
Inadvertently it also made "optimal" in Factorio be like: which one out of potentially hundred variants?