I studied on the BOOT disk the file boot.script and found in the value for bootargs the parameter disk=/dev/disk/by-id/mmc-00000_0x1537043d . I have the feeling there should be -part? appended, where ? should be 2 or 3. Both root= and resume= have -part3. respectively -part4 appended.
The disk parameter should be the disk, thats the root= parameter that needs the partition added. Anyway, the issue is way simpler. the Kiwi initrd destroys the hybrid GPT on resize, which causes the raspberry pi firmware failing to find the u-boot bootloader.
The fix is to restore that on first boot, so when you log in the first time, run this:
echo "r h 1 2 3 n c y 82 n 83 n w y" | \ /usr/sbin/gdisk /dev/mmcblk0
I'm trying to add that as a workaround to the image. Ideally there would be some feature in kiwi to do that :-/