A given FMU container inherits from fullmetalupdate_package_container_image.bbclass which defines a number of variables, especially some referring to files in the container recipe:
CONTAINER_STARTUP
RUNC_CONFIG
SYSTEMD_CONFIG
These files (located in the container's recipe) can change, and at the moment modifications are not taken in account when building a container. It might be a good idea to see if doing something resembling the SRC_URI_append incantation can work in this case, so as not to push stale versions of these files to OSTree.