Programming QSPI Flash

I would like to program QSPI Flash memory externally. That is, I have an external programmer (which is actually a software running on Raspberry Pi) so that I can program the QSPI Flash memory without applying the steps here.

For this, I just take the cli.bin and write to QSPI Flash memory page-wise starting from address zero.

However, I noticed that this method is not working and as I understand, the programming operation uses a different memory write scheme (rather than just incrementing the address for each write operation).

Based on my observations, the flash memory content differs starting from page 256 in Flash memory when I do the programming via the external programming method (instead of the original method).

Is there any description that I can refer to regarding the memory write scheme?