Hi. I’m trying to switch the mod settings from using pipe colors to using liquid colors, but I can’t do it because the selection menu is inactive.
I also noticed something else: if you build a regular pipe and an underground pipe, then use the upgrade planner to set the color “water” for each of them, only the straight pipe changes. The underground one doesn’t — you have to manually select the “blue” color for it.

Could you tell me how to adjust the mod settings so that the pipes use the liquid colors?

You can only change those settings from the main menu (they require a game restart to take effect, so the game won't let you change them while you're playing a save). But if you go out to the main menu, then go into mod settings, you should be able to toggle any of the options, and enable the fluid color recipes :)
For the planner tool, there are some per-player settings that you can change - but I'm not sure how much those will help since I'm not exactly sure what's going wrong there. I'll have to do some testing to try and reproduce it.