Hello,
Unfortunately, this problem is more related to how you program your FPGA, here is not a lot of what we could help you.
Seeing the link that you posted, I could see that you only configured the dtb to use the SPI interface. But, to program the FPGA you could use an SPI Flash, or simulate the J-tag protocol through SPI.
Please find more information about how to program the FPGA through an SPI Flash.
https://www.xilinx.com/support/documentation/application_notes/xapp1188-config-spi.pdf
Unfortunately, we are unable to assist you more, since this problem is out of our scope. I recommend you to go with Xilinx, they could help you with your problem.
Best regards,
Diego.