That's still a silly point. For security reasons a lot of people don't hook their source control directly into production web-servers, and instead deploy from a secured environment hooked into secure control onto production (which would still require something like e.g. SFTP for the actual transfer).
Regardless their point was poorly explained/explored.
Correct, workflow. Even with the tools themselves, rather than "best practice" it seems mind boggling using SFTP within the editor. With things like SASS, bower, grunt, npm and the like - it doesn't even seem like it'd be compatible.
Well I use a dev virtual server instead of a local vm. I enjoy working in a windows environment, but would rather not struggle with the discrepancies between running an app on windows with something like xampp vs apache on centos which are my web servers.
I use a sftp atom plugin to workin on/save to my dev server and just use ssh to do git/etc right on the server. I don't see how this workflow is very different than working locally and using a command prompt for all of your tools.