After some head-scratching, I realized the reason pin 4 seemed to be shorted high was that it's connected to STM32's UART TX via J5.
In the schematic, PMOD1 does clearly show how some of the pins are connected to the microusb port. However, it fails to show that some pins are also connected to J5.
It would be best if PMOD1's link with J5 was shown in the same manner as done with the USB pins.
After some head-scratching, I realized the reason pin 4 seemed to be shorted high was that it's connected to STM32's UART TX via J5.
In the schematic, PMOD1 does clearly show how some of the pins are connected to the microusb port. However, it fails to show that some pins are also connected to J5.
It would be best if PMOD1's link with J5 was shown in the same manner as done with the USB pins.