I've seen a lot of Docker images ignoring the Filesystem Hierarchy Standard (FHS). Most examples (some official) ignore the FHS. For instance, some may choose to put their binaries in /app and their data in /data, having an entrypoint.sh in the root directory and so on.
The intention of FHS is better interoperability of distribution and application. FHS compliance of a Dockerfile allows to change the Linux base image to another version or distribution. Such an upgrade may for instance be required to solve bugfixes of distribution packages.
It seems to be common practice to write non-FHS compliant Dockerfiles. Will this make maintenance more complicated?