I've noticed that the Underground Duct has double the fluid capacity of any other duct piece, but only ever seems to fill up to 50% under normal circumstances. It IS possible to force-fill it to 100% by attaching a pump or no-return valve to it, but it doesn't seem to full up "under gravity." I was under the impression that attached fluid vessels would attempt to balance their levels relative to maximum capacity, so an 800-capacity pipe at 50% (400 fluid) should be able to fill a 1600 capacity pipe to 50% (800 fluid). This doesn't seem to be the case.

Is this intentional?

It's because the underground duct is actually marked as "elevated 1" in the mod's data (vanilla undergrounds are marked as 0: ground level), so if you put a non-return duct before every transition from a corner, straight, or junction into an Underground, it will maximize the flow because the NRD (which is a pump internally) can lift the fluid 'up' to the Underground Duct's level. if it was -1, you'd be best served by putting NRDs after every transition away from underground

Yeah, I did notice that since, once I sat down to read the fluid container template API. That's really odd, though, because it causes underground pipes to behave like pipeline overpasses. I've made a local tweak to the mod, placing the pipe below ground.

The pipe is actually elevated by 2, as its height is hooked to the general multiplier. Setting it to negative that causes the underground pipe to behave like a sink - like the deeper section of pipe that it is. It changes how the system works, requiring non-return valves AFTER a pipe-to-ground section but it seems a bit more intuitive to me that way.

Vanilla fluid containers are all strangely designed, though. Vanilla underground pipes have a level of 0 and a height of 1 - identical to above-ground pipes. They exhibit no special behaviour, even though they probably should. Vanilla fluid tanks all have a height of 1 and a base area equal to their total capacity. They behave like very short, flat discs, rather than the tall tank the graphics suggest. I can't quite piece together why any of that is the way it is.