If you close the launcher, the window will disappear, however the process keeps running (noticeable on the icon and in the taskmanager). Some programs use that feature to close the gui and still work. But you cant reopen the gui without forcing the launcher to stop and then restart, either by CMD+Q or CMD+ALT+ESC on a Mac.
Edit: Can be clossed now, itr fixed in 0.6 (see: https://twitter.com/Dinnerbone/status/327726169485111296 )