I'll answer this question, in general. Hopefully, it will be applicable in your case.
In Deployment Manager, when you start a build it stores your artifacts in a directory specific for that pipeline and environment (Dev/Prod). When you publish from Pega, it stores it in the path described in the Repository rule. I'm assuming that these are two different paths and I would not recommend publishing directly to the path for your pipeline because that will likely just cause confusion.