- The pico BOOTSEL or the BOOTSEL from DIP switchs on the mainboard you mean?
The mainboard. The goal is to be able to put keyboard into flashing mode without opening the case and flip the DIP switches
Since the version 0.5, the internal RTC have the time and date exposed on the I2C bus
Superb. Also wondering, if we could hack the mainboard and connect VBAT to a coin battery – no external RTC module needed then!
GPIOs
Yeah I’m afraid those are all we’ve got, but nevertheless, the amount exposed via header equals those exposed from pico so I guess they will become useful, right?
… and, southbridge SuperIO, right? 
- Not sure to understand what do you want to do with programs and I2C registers…
This is pure fantasy, but if we first solve the progmem space issues (by switching to baremetal sdk), we can embed a micropython/basic interpreter in stm32, and transmit a program from pico to stm32.
It will then function as a coproc and run the program in the background, parallel to what pico is doing. Nothing compute-heavy should be done there since we will lose keyboard responsiveness, but I think it can handle some background logic, like maintaining persistent variables that can survive RESET and POWEROFF (with VBAT connected, stm32 has persistent ram).
A two-way fifo can be established with i2c registers.