The TCL script that you reference will create a bit-stream for the Zynq PL. If you use JTAG, you coal load this into the device.
But to generate a .bin file that can be programmed into the QSPI flash, I would suggest that you start with a PetaLinux project that you can create using the BSP minized_qspi.bsp. The BSP is downloadable from the MiniZed Reference Designs page. There are a number of documents on that page that describe the process of using such a BSP. Once you can use the reference BSP, you can modify the bit-stream and behaviour with your own design.