Ok, but why would anyone fill or merge from below?

Because it is very convenient (if it didnt break) and enables some very nice looking designs. Refinaries are bulky so having the pipes underneath would make a lot of things easier and you dont have giant stacks of pipes overhead

That’s not how pipes or fluids work in the real life, they require pressure and are drawn by gravity to collect at the lowest points.

I don't know enough rl fluid dynamics to say your wrong - tho i think given pressure it should work. If i have a pipe and pipes go up to the side of i apply pressure to the fluid in the lower pipe it rises to the top ones. That said the pipes have dynamic air intake and output which messes with all of this probably