Ahoy. Seems like I found a solution to both use --mobile-server to connect to a remote server, and get hot code pushes from a server holding your actual Cordova-specific code.
Package here: https://github.com/gwendall/meteor-remote-autoupdate
What it does is allowing you to define the URL where Autoupdate will watch code changes from. Would be nice to have such an option in core though. Tested locally, seems to work fine.