Looking at the MKR1310 schematic, I don't think that will give a supply to the 5V pin. The MKR1310's DC-DC converter takes the voltage from VIN and produces a 3.8V output which feeds the 3.3V linear regulator. The 5V pin isn't fed any voltage in this configuration.
What I can't figure out is whether it's ok to power the board using the 5V pin, if you are supplying 5V externally. If so, that would also supply 5V to the i2c port.