Which is what flatpak will always do unless provided with the --user flag.
By default it operates in system-wide mode, which is different from "root's".
flatpak list and sudo flatpak list will both show you what is installed system wide, and flatpak list --user will show you your user's, and sudo flatpak list --user will show you the root user's flatpaks installed in per-user mode (of which there are typically none).