I check the blueprint, and i think, that for 5V boards, if You use 5V power source, this regulator on board have slight voltage drop, and arduino will not have exactly this same voltage, bypass jumper j1 is to go around that regulator.
But if You will use another source, like 6V to 12V beater is disconnect that jumper to get on board 5V.
On schematic is misleding peoples including me that jumper is to chose what voltage i want operate. This is true for board with 3.3V if Your source like USB is connecting to Your board. Then this jumper should be always be opened.
But if You have board working on 5V, and You want VCC pin have more juice to drive external modules, and Your iinput voltage is already regulated to 5V, like from usb, then You have an option to bypass that regulator.