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Hi,
You are absolutely correct about the pin configuration. The pin numbers in the documentation for you Fipy are the correct ones
https://docs.pycom.io/datasheets/development/fipy/
The Expansion board pinouts refer to an old standard we no longer use. Your offline expansion board should have the correct labels.
To answer your first question, you can look at one of the tutorials here: https://docs.pycom.io/firmwareapi/pycom/network/wlan/
And connect the second uart (TX1 and RX1) to the external microcontroller.
The pins connected to Lora/Sigfox are internally connected in the device. On a WiPy, this is not the case, as it does not contain a lora radio.
You will indeed not be able to use lora and SPI at the same time, but you can learn more about that here: https://learn.sparkfun.com/tutorials/serial-peripheral-interface-spi/all
Hope its still useful to you!