I now consider the wiring definitive.

DS3231:

SDA to GPIO10 (i2c1)

SCL to GPIO11 (i2c1)

3V3 and GND taken from extra headers soldered on the keypad base.

RGB Keypad: 

Default wiring, no change

Pico Display:

GPIO 16 (LCD_DC) and GPIO 20 (BL_EN) unchanged

Reset unchanged, as 3V3 and GND

LCD_CS connected to GPIO 21

LCD_SCLK to GPIO 26 (SPI1)

LCD_MOSI to GPIO 27 (SPI1)

Extras:

Buttons and RGB lines, that are on the opposite row can be wired as intended: they are not used by anything else.

Here is a preview of what it now looks like
https://twitter.com/Angainor15/status/1359431057611882498

*Update 2021-03-22. Fix wiring.