The programming flow is to set the boot mode pins to JTAG and issue a PS_POR_B before programming the QSPI.
The programming flow also requires you to specify an FSBL that runs on A53 (an FSBL running on R5 will not work) to help the programmer to initialize the system.
Note: This is not a silicon requirement, it is a tool limitation.
Future Vivado releases will not have this limitation and it will be possible to program QSPI in Production Silicon when booting in QSPI boot mode.
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