Hi @tp_24,
actualy you are correct. Lot of pin muxing, clock and power configuration is done in BoardInit.c. I guess you could also need to modify U-Boot to be safe.
BoardInit.c (Part of UEFI that sets up everything for Windows drivers) is in adjacent folder to the ACPI tables:
mu_platform_nxp/NXP/MX93_11X11_EVK/Library/iMX8BoardLib/iMX8BoardInit.c