To customize the board i think a firmware configuration file could come handy.
The file should stay in the botsel part of the storage and should allow some basic configuration of the device.
The configuration should be applied on each firmware update so the configuration will always be the same even if the defaults in the firmware itself changes.

It could look like this
`
[GENERAL]
FileSystem="FS Label"

[USB]
USB_VID = 0x239A
USB_PID = 0x804C
USB_PRODUCT = "PyRuler"
USB_MANUFACTURER = "Adafruit Industries LLC"

[ENDPOINTS]
0=CDC
1=Storage
2=Keyboard
3=BootKeyboard
4=Gamepad
5=MIDI
`

Reference:
#4191
#1136
https://learn.adafruit.com/welcome-to-circuitpython/the-circuitpy-drive
https://learn.adafruit.com/how-to-add-a-new-board-to-circuitpython/customizing-the-board-files