> You sure it's not booting kernel from eMMC, and the rest of the userland stored on NVMe?

I'm sure, since my RockPro64 has no eMMC (I didn't order one, and I just checked that my eMMC slot is empty).

I have Tow-Boot installed on my SPI, which when booted jumps to the NVMe device.

My initrd has modules "nvme pcie_rockchip_host phy_rockchip_pcie" which are needed for Linux to detect and then mount the rootfs.

  $ mount
  [...]
  /dev/nvme0n1p1 on / type ext4
  /dev/nvme0n1p3 on /boot/efi type vfat
  [...]