YES. We have identified the root cause of this issue.
The issue is that for JetPack 5, NVMe and USB drivers are integrated into NVIDIA’s downstream kernel, and built directly into the kernel image; for JetPack 6, in order to be compatible with upstream kernel, a lot of drivers are pulled out of kernel source, and built as kernel modules.
Therefore, initrd must contain these drivers for NVMe/USB to be mounted as rootfs during booting, but initrd does not get updated during kernel building/flashing, and the kernel suffixes (5.15.122-tegra/5.15.122-rt-tegra) do not match, so drivers cannot be loaded.
A temporary solution would be to copy and unpack the initrd image to the host PC used for building kernel, change the folder name, replace those .ko files with the correct one, pack the initrd image again.
I don’t see any issue with RT patch + JetPack 5.
This is not related to flashing, so please file another topic.