MDBT42Q page documentation clarification needed

wondering why the h/w USART has a color key but the h/w SPI and I2C do not.

As the comment under it says: "...Unlike other Espruino boards, these peripherals can be used on any pin.". There's no point me putting all USART/I2C and SPI tags on all pins :)

my belief is that the USART Rx pin is checked, and if in a specified state, BLE is then not available with the IDE

No - BLE is completely separate to Serial.

If you force the console to Serial1 with Serial1.setConsole(true) then yes, the console will go to Serial1 and not Bluetooth, so the Web IDE won't be able to connect. Bluetooth still works though and is then available for use by your code.

I think what you actually want is Bluetooth.setConsole(true) so let you use Serial1 without the REPL interfering with it, while allowing the IDE to stay connected over BLE

as when I attempt not to use the h/w USART, I get this error

Yes, start another thread for this and post your code - but note that software serial really isn't that reliable right now so you may hit issues.

Honestly, if you have one-time configuration to do on the GPS, then use the USB UART device they recommend with the app that they provide for it. You're just making your life needlessly difficult trying to go through Espruino.