I'd suggest you maintain your own separate PFC project in source control.  That will ensure that stuff that your company considers its IP doesn't get mingled with the open source project.   Create a fork or the open source project and add stuff to that you want to contribute to open source, but don't mix the two.

As for applications that depend on PFC, the answer "it depends".  If you're going to be doing automated builds from source control you're going to need the PFC layer as part of the apps source control project or you'll want to compile that to PBDs and then reference that from the target application.  If you're not doing builds from source, then you could just reference the common PFC layer from each application and just not put it into source control within that applications project.

Also, the question is: how often is your own PFC/PFE layer changing?  If you're making routine changes to it, then it makes more sense to have it as it's own project.  If it's quite stable though, you could just include separately in each of the applications.  You'd have to update it in each one later if you did modify it, but it you're not making a lot of changes that's manageable.