I made a fresh build system on my development machine. My build ran a couple of times without above mentioned patch, but broke because it was not applied. After applying the patch my build worked, but the copy device tree issue remained. (But not on the build server) I then ran ./oebb.sh update to make sure everything is cozy (which removed the patch mentioned above without me realizing) and miraculously the build continued to succeed, but the device tree issue remained. I suspect I broke sstate by doing this. My sstate is not shared between dev and build.

Therefor, I suspect that the issue was generated in house. Regardless, the rest of create_image.sdcard does not make assumptions as to pwd, so I figured the patch is needed for completeness.