Trying to use pin D3 as SPI2_MISO alternate function does not work, the pin D3 switches to the previous alternate funtion (SPI2_SCK).

This can be fixed by removing the AF3 declaration out of the stm32wb55_af.csv list:
PortD,PD3,,,,SPI2_SCK,,SPI2_MISO,,,,,QUADSPI_BK1_NCS,,,,,EVENTOUT, (Original)
PortD,PD3,,,,,,SPI2_MISO,,,,,QUADSPI_BK1_NCS,,,,,EVENTOUT, (fix)

But this causes the Pin D3 incapable of switching to SCK mode.

This is caused by the definition of a pin list in spi.c (line 294), not a function list. In the pin list, the actual output pin is defined, but the information what the pin should be doing is not remembered.
A sollution could be the sequnce of the list, it can be defined to hold the function. The function mp_hal_pin_config_alt then should be told what the pin function should be.