Thanks for the comprehensive reply.
I had looked a the STM32WL5E datasheet but there is little mention of how to address the LoRa device. However, the Reference manual RM0453 says this about the STM32WL5X ;
Section 5.8 of the reference manual also gives the opcodes used for the access to the radio, and the ones I checked are the same as the standalone SX126X opcodes. So it does look like the STM32 silicon is talking to the (standard ?) SX126X silicon over an internal SPI, it even mentions the Busy pin. So presumably this SPI interface is accessible to other code (libraries) running on the STM32 core.
I could not find where in the rak_rui core the API code was actually talking to the SX126X.