Site config with shared core

Our studio has a site pipeline configuration that’s shared across projects as described in @philip.scadding’s thread here: Recommended way to share/update pipeline configurations between projects?

One side-effect of using the (path) descriptor to accomplish this is that the desktop bootstrapping is ignoring the configuration’s install_location.yml and pipeline_configuration.yml files (by design presumably) and foregoing loading core and apps from the install location on our network. Instead, it’s downloading all these to a local bundle cache in the user’s home directory. While this technically works, it means that we’re completely foregoing using the shared core we specifically set up, with some nasty side effects (e.g. we’re unable to bootstrap TK on the farm without explictly adding the location of the shared core to PYTHONPATH).
Anybody out there have any similar experiences? Ideally we’d like to have our cake and eat it too: keep a shared site config and continue to use a shared core.