Pin definitons for 40pin header
Do you have the pin definitions you use for the 40 pin header? I wonder if using two of them on opposite sides of the board would make for a more robust mechanical design.
Your work is similar in some ways to some work I tried with https://github.com/rosmo-robot/Feather-Bit/tree/main/v1 to create a series of daughterboards. I was basing it around the feather rather than the Pi as it seems most Microcontrollers were available in the feather footprint.
I'd be interested in revisiting the concept, perhaps based on reusing two 40pin RPI headers as suggested above. Very rough concept below.
- One header retaining the RPI pinout for pi-hats
- The second header retaining the RPI 5v/3.3v/Gnd locations but optimised for microcontrollers, SPI, UART, Ethercat etc etc
Edit: Actually looking at Sparkfun Micromod it might be a really nice starting position.
We could just edit this board: https://www.sparkfun.com/products/16885 to have the 2x 40pin GPIO. Very quick & dirty concept in Kicad: 
Here are the pin definitions
Do a daughter board for their function boards (Inc ethernet) https://www.sparkfun.com/micromod#main-boards.
This project is interesting too: https://github.com/MDCservice/EsPiFF
The motherboard would be pretty minimal, to keep cost low, relying on daughter boards to provide most functionality. Maybe include a Qwiic socket on the motherboard. Perhaps an unpopulated UEXT https://www.olimex.com/Products/Modules/ too
I don't know if this is too far from your original concept to be excited by?
As an aside I could put this pinout on the rear of this little robot