How come the microcontroller of this board is being powered in this configuration?
You don't provide any details about your FTDI board.
But if an USB to serial converter has a 5V pin, there is no reason to assume it is a power input.
The 5V pin would be expected to give out the 5V USB supply provided by the PC.
When that ia connected to the 5V node on the Nucleo it will power it up. Same way like connecting it directly to USB from the Nucleo USB. So don't connect two supplies to it.
You can verify this by reading the USB serial adapter manual. Just make sure the TX/RX pin use 3.3V voltage levels instead of 5V. Some, but not all MCU pins are 5V tolerant.