The view we seem to be edging towards is that it may be most appropriate to treat the "pip in the system Python" use case as an advanced use case, because the failure modes when the system package manager and pip get into an argument can be a bit ugly, and resolving them can be very platform specific. Even though things probably won't go wrong in a lot of cases, when they do go wrong, they're likely to wrong in a way that is hard to understand and fix if you're not an expert in the vagaries of Python's import system.
It's also where most of the complexity in PEP 439 lies: how do we keep the bootstrapped pip up to date? Do users have to run "pip install --upgrade pip"? Does it happen automatically when a maintenance release of CPython is installed? Do we bundle a particular version of pip with the installer binaries, or just offer the option to grab the latest from the internet as part of the installation process?