I saw a few projects where "developers" were not religious about tech.. they still using ftp for php files deployment, "BUT HEY! THE SHIT IS DONE!" :). I don't want be sarcastic, but i think every startup team should have at least one engineer who will know what to do, at every iteration of the project.

Yup. 'sama tweeted something similar about users not really caring about underlying tech. None of it matters if users don't love the net result. JFS - just fucking ship. Worry about delivering a compelling product, why you are building it and monetizing to stay fucking alive. Bikeshed on which testing framework to use another day.

whats the "preferred" way nowadays? commit source using git to server and let it autodeploy?

If you can deploy: fast, atomically, without downtime and can revert your changes at any given moment, then it is not that important :)