Just got a time slot for experiment, sorry for delay.
Looks like typo - should be J7.41 (SCLK) ---------------- Pin23 (SPI0_SCLK), could you edit your post, please.
My setup is as follows:
1. R184 resistor soldered (to supply on-board buffers for data lines);
2. Board is powered from external 5V power supply;
3. USB MCU is powered from USB (UNITE7 is connected to the RPi via using USB cable);
4. USB MCU is reset (SW RST switch is set to "ON" position);
5. Wiring between RPi and UNITE7 is as above except SAEN is connected to the ground instead of RPi' GPIO12
The reason of item 5 is that SAEN line is not controlled from RPi side - it looks like it is an input, not output. Hence configuration van not be uploaded.
When I run your software, I can see an activity on DIQ2RX_* lines. So, it looks like everything was OK, except SAEN line and you have to connect USB cable just to power-up the USB MCU (it will supply the SPI level buffer between LMS7002M and USB MCU or J7 pinheader).
Let me know if this helps.