Hello!
First off I have used your mod for a very long and have always loved the extra functionality it provides in the game.
Today though i might have found something that I don't think should work the way it does and scrolling through the past discussions I did not find it mentioned.
Recently I have started making setups where everything is legendary with maximum throughput per building in mind and thus I found a wall that for a long time seem to have misunderstood. The wall being that no matter what setup I use I could not get more than 6000 liquid per building either as output or input. 6000 being the maximum throughput of a liquid connection of a building per my reddit/wiki education.
After testing without the mod I have found the results to be different which leads me to believe that the mod changes some building logic that makes it so a building has a singular shared outputs/inputs and thus limiting it to 6000. I also tested without any mods active apart from this one and the result was the same.
Here are some pictures to show what I mean - https://imgur.com/a/mod-lPfrf0B
The first image labeled "With mod 1" shows me hovering over a pipeline connected to a foundry. The pumps here serve a double purpose: the first emptying the pipe so the foundry can reach higher output since the amount of liquid it can output is proportional to how empty the pipe is( in this example though I have not shown it the pipe is around 1-2% full, meaning that there is no realistic limitation on the side of the pipe). Secondly through screenshots 2 and 3 I am showing what the actual throughput of the foundry is. The combined throughput of the two pumps is around 5500-5700 maximum while the calculator at the top left shows the true production of the foundry being at 9922. I have not added screenshots of the other two pumps simply because they are not operational. I have done other setups with more pumps and adding the other two connections but the result remains the same. In my head it is like there is now a central invisible liquid connection where the four visible connections actually connect to. Meaning that the top left and top right connections actually are one instead of two separate which explains why the limit is 6000.

Without the mod the setup remains exactly the same shown in the second set of 3 images. But on the first image labeled "Without mod 1" there is now a difference and it shows why having two different connections matter. So lets compare. In the image "With mod 1" the pipeline, the building and the second pipeline are highlighted, but In image "Without mod 1" only the pipeline is highlighted meaning that the two pipelines are now separate, each now with their own limit of 6000 liquid. And that is also confirmed in screenshots 2-5 showing all four pumps now operational and the building is working at full capacity.

In the last two screenshots I have drawn with red lines the way the connections inside the building seem to be right now with 1 "true" input/output in the first and correspondingly how it could be changed as to retain the vanilla 2 "true" inputs/outputs while still having the passthrough function.

Some disclaimers and extra info:
I haven't tested every single possible building or recipe though I easily found an example where the input is limited that being the Ammonia rocket fuel recipe which when at 300% productivity and speed modules in the surrounding beacons and inside the Cryogenic plant requires 9000 Ammonia which again I found to be impossible to input and as such I use two buildings limited at about 4300 input each.
Secondly since I don't know whether the mod can be changed adding a comment in the information section could save same hair pulling on the user side. It definitely would have done so for me. And ultimately I'd still use the mod because in my view the passthrough effect is nice to have even if I have to put some extra buildings down in specific cases.
Lastly I have no idea how the factorio mods are made and work so if what I am writing here turns out to be the ramblings of a madman just tell me so and ignore everything here :) .

Apologies for the small wall of text.

I am a little confused at what you are questioning, or think this mod is changing.

Can you please provide me:
1. a succinct (brief and clear) outline of the issue you are observing - I have read through your post multiple times today, and I cannot determine what you are are actually asking from me.
e.g. Foundries producing molten iron produce molten copper when you loop the outputs back into the inputs in this configuration. (clearly something that shouldn't happen).
2. a minimal save with one (1) or more setups that you have tested.

tldr is vanilla foundry has 2 separate fluid outputs of 6000 each and combined gives maximum throughput of 12000.
With your mod the foundry is limited to 6000 which probably means that your mod somehow combines the 2 outputs into one and thus limits the foundry to 6000.
As for a save with a setup I can make one though I have no idea what file sharing services people use nowadays. You are going to have to point me to one if you want a save.
Though the setup really doesn't matter. The whole point is to juice up a building to the max and in this example a foundry with the iron ore+calcite into molten iron recipe because it has a very high throughput and then simply see how much you can realistically get out of it. Because in this instance the foundry working at 100% produces 9922 molten iron but you can not get more than the theoretical 6000.In reality the building is working at around 60% . Which is why I am screenshotting the pumps. To show how much is really coming out of the foundry. Then you turn off the mod, load the save and you will see that the pumps are now pumping more liquid and you get the full 9922 molten iron out and the foundry is working non stop now.

I should note that with a pure vanilla setup you wouldn't actually see the foundry work at 100% because the buffer of the foundry is too small. With a pure vanilla foundry you will need to add more pumps than what I am showing because of the small buffer and the 2 or 3 pumps per side simply can not keep up. I use a mod called "Large Foundry Buffer" which smooths that transition and reduces the amount of pumps necessary and the foundry works at 100%.