When trying the planner with my base everything is replaced by the bots automatically (even though I didn't build a single colored item yet) but not the normal pipes: https://imgur.com/a/LxnAmky

Hi Maeximus,
In version 0.0.2 I've made some changes, hopefully it's less confusing. I've added a mod setting to choose between a "best guess" mode and a "perfect match" mode for the planner. Best Guess attempts to match the fluid color to one of the standard rainbow color pipes, while Perfect Match uses pipes that have the exact color as their contents.
If either of those pipe recipe types are disabled in the color coded pipes mod settings, robots will use base pipes to build the colored versions.