Until there is dedicate DTB you can automatically run the required command.
Create file /flash/user-update.sh with this content
mkdir /dev/mnt_tmp
mount /flash/SYSTEM /dev/mnt_tmp
export PATH=$PATH:/dev/system_mnt/usr/sbin:/dev/system_mnt/usr/bin
export LD_LIBRARY_PATH=/dev/system_mnt/usr/lib
fdtput -t s /flash/dtb.img /soc/pcie@f5000000 status okay
umount /dev/mnt_tmp
and pcie will be enabled automatically after each update without manually running any command.