This is a pretty simple recommendation. Right now, the Pipe to Ground segment has double the height of all other pipe segments (sans the pumps), which doesn't make a lot of sense visually. It's not a taller segment. It seems like it's intended to extend a level above ground and a level below ground (hence the double height), but if that's the case then it needs to have a height of -2. Or more specifically, a height of "- settings.startup["fmf-duct-base-level-multiplier"].value/2".

Currently, the pipe to ground segment is impossible to fill due to its height. Only pumps can fill it. With this change, it becomes a fluid sink/trap, which requires pumps to pull fluid out of the recessed pipe effectively. This seems like a more natural state, though it may affect throughput.

edit
Basically, the "underground" pipe behaves like a pipeline overpass, instead. Difficult to pump fluid into, forces fluid out. It ought to act the other way around - draws fluid in, difficult to pump fluid out of.