sequence only works on commands that operate on the view, while save is a window command, so it doesn't know what to do with it.
Your best bet is to write a quick python plugin to do this, something along the lines of:
import sublime, sublimeplugin
def run(self, window, args):
window.activeView().runCommand('sequence', 'removeWhitespace trailing', 'removeWhitespace extra'])
<binding key="ctrl+s" command="stripAndSave"/>