• The version of FMF and Factorio:
  FMF: 1.2.8
  Factorio: 0.18.34-2
• Other mods in the game (loaded with FMF):
  https://pastebin.com/5fkeyh0J
• A brief description of what you are experiencing:
  The capacity of (long straight) ducts are limited after an underground duct, possibly to the capacity of the underground pipe, or to the 50% of the duct itself. In other words, when the straight duct before the underground duct is filled to 388 of 400, the underground duct is filled to 794 of 800, the long straight duct is only filled to 751 of 1600. This only happens if the fluid is extracted by outtake endpoints down the pipeline.
• A brief description of want you are expecting
  I expect the duct after the underground duct to be nearly as full as the underground duct before it.

I use the before-after words because this is a section of ducts that are made to be one-way.
You can see a few screenshots of the setup here: https://imgur.com/a/5TznXiJ

The real throughput is right, this is matter of fluidbox height, I can't hide or adjust the tooltip but for make the fluidbox fill up right, will slow the throughput .

You mean the throughput is lower because the inderground ducts are not full? This is what I though to be the issue, too. But why isn't it full? The pipes leading to the source tank are full, and both the intake and the regular pump is not even near their full capacity

This is a bit difficult to explain, summary, Factorio give an higher throughput power to high fluidboxes, the problem is that if exist an high difference from two fluidbox one can't fill the other. As said, I prefer fast fluidbox (as the mod try to give) instead of right tooltips.

So basically it slows down the flow because it's underground, right? What could I do to have (near) maximum flow when I need to get fluids from one side of a rail to the other?

We are having the same issue as MPeti1 here, every time we use the underground ducts the flow rate drops extremely slow. What is the point of this mod since it seems like you get much lower flow rates than vanilla when using underground pipes/ducts.

i too am having this issue, and as I understand the response, it is just the way factorio is, and if that's the case I would rather go back to vanilla pipes as I see no benefit to using this mod. Sorry.

If u all having less throughput than vanilla pipes, probably all are using a very low quantity of pumps in in networks or ur networks are too big and need to be segmented.

Ok I have decide to boost the underground ducts, enjoy!