I've reverted my configuration a bit to better reflect the one shipped by NXP and very likely have found the culprit.
The imx-boot-imx93-custom-qsb-sd.bin-flash_singleboot is build with imx-boot recipe, which builds the binary based on u-boot and u-boot-imx recipes. I've tracked the cause of the problem to the changes in the U_BOOT compilation config options. A custom fragment.cfg is applied to u-boot-imx binary, disabling the CONFIG_ENV_IS_NOWHERE option, just like below:
# CONFIG_ENV_IS_NOWHERE is not set
Without this fragment.cfg file in the u-boot-imx_2024.04.bbappend recipe, the u-boot image burns into the board without any issues. With, the problems explained in the previous posts occurs.
Is the NXP i.MX93 board not compatible with CONFIG_ENV_IS_NOWHERE? If so, are there any alternatives? All I want to do is to store the u-boot env and have access to it.