Further research shows that while the RP2040 is a fantastic chip, there are better off the shelf components that would help me materialize my goals. Specifically
this off the shelf microcontroller. It just fits in the opening of the plate cutouts where the current MCU sits, has an integrated USB for programing off board/troubleshooting, it comes with native Bluetooth/battery and I don't have to solder any SMD components. The ESP32 also seems to offer more GPIO for future developments and features, like an SPI display or rotary encoder.
Using this off the shelf chip, I should be able to use Elmo's design as a reference to create a carrier board/PCB for the switches/LEDs to mount to. The only downside is there are 27 not 28 pins. This means I will have to remap the matrix to 6x20 vs 6x21 if I want enough pins for the LED indicators. But if this works out well it would be easy enough to create a new PCB that accommodates all the features I am looking for.