Hello!
Love the mod, thanks for making it.

If possible, I'd love for a toggleable option for colored pipes to be made back into regular pipes on pickup, similar to the toggleable option in Fluid Control.

There is an option to hide the color-coded recipes. With that on, you can use the planner tool or the chat command to color code your pipes, and the robots will use normal pipes to build the colored ones, and pickup normal ones when mining them

I question on this topic:
Is it possible to have the same entities as the original one? I guess If I remove the mod, all the pipes will be gone?

Yes, if you remove the mod, all the color pipes will be gone. If you want to remove the mod, I'd suggest to run /unpaint-pipes to change them all back to the original base unpainted version

Thank you!