Purpose of level-shifter with same in and out voltages
On the full schematic there is an interesting note that starts:-


  due to the serial lines being able to back power the cpu...


The STM32F407 MCU is only rated for an absolute maximum of 5mA injected current per pin (-5mA, +0mA on 5V tolerant pins), so if it was powered through a UART pin it could easily be damaged. The TXS0108 level shifter is rated for 50mA per input, so it is less likely to be damaged by eg. connecting an RS232 serial device (which might put out +-12V at 15mA or more). 

Another reason for buffering the serial port lines could be to make the MCU more tolerant of EMI. Autopilots are often used in harsh environments with nearby rf transmitters and high power brushless motors. An EMI induced glitch that caused the MCU to freeze or go crazy could crash the drone before it had time to recover.