I can't see any difference in the device tree between the versions in regards to how system is mounted so this maybe a twrp issue if rebooting to recovery after wiping data to remove encryption doesn't allow you to mount all partitions correctly and swiping rigjt to allow modifications to system partition on first run of twrp.I had an issue with version 3.4.0-1. When I tried to wipe or flash system partitiion I got following message:
I also could not unmount system partition from mount menu: I touched the tick next to "system" but it kept being marked. Other partitions mounted/unmounted ok.Code:
Failed to unmount '/system' (Device or resource busy)
I tried twrp-3.2.3-0-cedric.img. This one did not have the issue. I wiped the system partition. After reboot I flashed 3.4.0-1 and now flashing works.
The system partition was stock firmware (never flashed yet). Seems like 3.4.0-1 has some issue with stock system partition.