The Flatpak setup script places 60-ddcutil-i2c.rules and ddcutil.conf from the ddcutil project into /usr/lib/udev/rules.d/ and /usr/lib/modules-load.d/.

Usually /usr/lib is used for distribution-specific (and/or native app-installs) configuration files and /etc/ is used for install- or user-specific configuration files. With this script living outside of the Flatpak install/uninstall process and these files possibly conflicting with another version of themselves from a native installation of ddcutil, I see an argument for moving them to /etc/udev/rules.d/ and /etc/modules-load.d/. Files in /etc override files from /usr/lib (if they are named the same).

There are other apps with similar problems (YAFI, fan-control, StreamController, etc.) doing the same.