this is a typo in the documentation: 3.3V outputs are only available for MBHP_CORE_LPC17 due to a chip limitation (erratum).
MBHP_CORE_STM32 and MBHP_CORE_STM32F4 configure the output pins in open drain mode, which means that the pin is in high impedance state if no MIDI message or a logic-1 is sent. Via the 220 Ohm resistors and the optocoupler at the receiver side, the voltage level will be pulled to ca. 4..5V.
The MBHP_MIDI_IO board has an additional 100k pull-up resistor to 5V, but this one is only used to ensure a proper signal for the LED indicators.