Do you believe that the schematics / complexity could be decreased by using QMK to power the MCDU ? As I understand, the MCDU is supposed to be a very simple Human Interface Device (HID) without any software logic (simply plugged into an FMS)

This is but a suggestion, as I am not able to properly gauge the pros / cons of using that system compared to the one you made with the RPi Zero. However here is a quick run down

Pros

• Popular high end mechanical keyboard firmware
• Lots of tools and documentation
• Off the shelf (cheaper) micro controller boards
• Already support for (some) screens
• Can be used as a generic keyboard
• Can be easily reconfigured by the users

Cons

• Very limited flash memory compared to RPi (SD card)
• Not compatible with all the work done so far (except keyboard wiring)

Display

• Have to add support for the current screen
• Might require a separate connection + driver for the screen
• Could create a tty or serial connection to forward characters onto the terminal-like display (I believe it could be done through the QMK microcontroller)

References

QMK programmable buttons
QMK Joystick (interesting for other systems)
Compatible microcontrollers