Just an impression, but seems like there is a failed concept due to not being able to utilize the buildings at the beginning. Since you can't get fluids into them until after you research a bit, you are forced to landfill and work outside to get research unlocked. Perhaps building fluids should be already enabled, or early on research with basic pipe. Very odd that you have these nice building's as part of the concept, but can't really use them.

Two things:
- why would you need to get fluids into the building? While fluid transfer is locked until later the actual concept is that you dont build anything in the original 'island' and instead everything is built internally in the buildings themselves.
- where did you get landfill from?

Oh, and just in case: both the regular offshore water pump and the seafloor pump are peaceable on land without requiring water - this means that you dont need any water tiles anywhere and are free to build your factory fully inside the buildings without being constrained to how many pumps you can place in the limited space of the original island.

I had the same issue and found out the reason after a couple of hours of landfilling the starting area... If you don't like / don't use all the required mods (I disabled FNEI and Helmod in my playthrough) the custom scenario doesn't get loaded correctly and you get to use the provided landfill in the starting area, and you cannot place water pumps inside the factorissimo buildings.