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The AN84868 project uses SPI Interface as well in addition to UART. From Table 7 of FX3 Datasheet, when both SPI and UART are used, the UART pins are mapped to GPIOs 46 to 49. But when UART interface alone is used as in An65974 project, the UART pins are mapped to the GPIOs 53 to 56.
In your custom board you would have connected the UART pins to 53 to 56. So you did not get the debug prints.
However, in the AN84868 project, after you have switched to Slavefifo mode (after finishing configuring the FPGA), the SPI is disabled, and now you can get the UART Debug Prints from 53 to 56.