Hey Lasciva, it appears that this request might not be possible. If I'm understanding things right, robots can only use a single item to build entities. I am guessing that in Flow Control, even if you have the special pipes available in your logistics system, the robots will only use normal pipes to build the special ghosts.
That also applies to the item you get when you pipette (Q) a pipe - if I tell the game that the colored pipes are buildable by normal pipes, you will get a normal pipe in your cursor when you pipette it.
A potential workaround could be that I add a mod setting to allow robots to build colored pipes using normal pipes, and then I write some runtime scripting to update your cursor to the colored pipe version when pipetting. I think this is close to what you're asking for, but would mean that even if you have colored pipes in your logistic system the robots would be unable to use them. This might work, but I don't love it.
I would suggest using another mod to increase inventory size, or setup a little mall to make all the colored pipes available to your robots.