Hi Tania,
with the INTF_SEL pin configuration shouldn't be a problem. If you switch the SW2 for SPI interface, the INTF_SEL is connected to VDD through a 10k pull-up resistor. But there is no harm to bring the VDD directly to INTF_SEL pin.

Please remove the jumpers from the J7, J8 and J9 headers.

Please remove the R3, R1 and R4 pull-up resistors. They are not necessary for the SPI interface if your MCU have push-pull inputs/outputs pins. They are needed for I2C interface only.

Please send a read command once again, now with the correct CPOL=0 and CPHA=0 configuration.
Please send 1001 0011 0000 0000 0000 0000. Please share a scope of the SPI pins.
With Best Regards,
Jozef