When using --src-imgref, bootupd fetches the static configs from the host rather than the destination container.
An easy way around would be to chroot to the deployed path before the bootupd invocation (this would have the added bonus of using the bootupd binary that is shipped into the image rather than the one in the host).
e.g like in https://github.com/osbuild/osbuild/blob/main/stages/org.osbuild.bootupd
When building FCOS i got only the configs that exist in COSA rather than what is in the container (thus missing the ignition fragment)
Related: #1455