Its considered best practice to locate small parts in the middle of the jaws. Its kinder to your vise jaws & and actually holds more securely because of the location of lead screw. When there is no other option people block up the other end. Obviously it has to be very closely sized so either sacrificial stock or mini machinist jack. Making jacks is on my to-do list as well. I have used makeshift ones from a cap screw & double nut (longer coupler nut on end & regular nut to lock it). But a bolt head & shank probably don't provide good contact like the jack pad. Anyways you very lightly tighten the part side, then jack the bolt assembly nut so its firm in the jaws, then tighten the assembly. Always check the part is secure before milling because its possible for things to distort & move.
BTW for squaring & surfacing I use my insert mill head a lot. It provides an accurate surface & as good or better finish as any fly cutter I've messed with. But it can also take material down pretty good too. I square off the ends of longer stock with an endmill exactly like you are showing because there is no other good way, but whenever possible I prefer to mill across it with the bigger tool for best surface & dimensional control.