I’ve been working hard these past few days to migrate away from WPEngine, moving to DigitalOcean, so I can’t help you there, but as to the dev questions:
The VirtualBox Vagrant images should stay running so long as you don’t restart the computer, but the last time I checked, you couldn’t run multiple ones at the same time without editing the ip address during setup, and I was never sure how to do that. So my workflow is to cd into the directory of the site I’m not working on, vagrant suspend, then cd into the folder I am working on, vagrant up.
You could create a bash script that does it all for you, maybe take some variables to begin (site to suspend, site to launch), and save yourself some typing.
As to developing with Sage, I still find this hard to deal with, I think at a certain stage, you just need to let go of keeping it inline with the repo, and make it work for you. Anyone else have input?