Ok, I see the problem, and it's not caused by my mod, but by the new fluid system of Factorio 2.0.
With the new system, if a fluid container is filled less than 20%, pumping out fluid will get slower as it gets closer to 0%.
You put a crazy capacity on the storage (2 billion), so of course it will be extremely hard to empty if it stays very close to 0%.
Use a more reasonable and realistic capacity and it will be ok.
https://factorio.com/blog/post/fff-416