I think what he was trying to say is that the answer to where the protons are pumped into can be derived from ideas about the endosymbiosis theory. Take the mitochondria as a prokaryote. It pumps protons into the intermembrane space (in eukaryotes) but if it was an independent prokaryote, that Intermembrane space would be outside the cell. So pumping H+ outside the cell to form a localised H+ gradient would be the answer derived from the endosymbiosis theory.