I ran into a situation a few months back where I had a factory assembly with a base pipe run in it.
Because you can only (at the present) create one base pipe run and the pipe run on the other configuration
in my factory needed a different one, I was not able to accomodate the second configuration with the pipe run I needed.
In fact on the second configuration it would turn the associativity to "OFF" which messed with the pipe runs as well.
I have posed this scenario to my VAR and they confirmed that what I was trying to do can't be done and they would be looking into this. Seeing this was a couple of months ago I am assuming there is no way at the present to do this.