For fun, a shell script for the same functionality:

#!/bin/sh
br="$(printf "\n")" # Obtain a line-break

# If RM_CMD is unset, use trash-cli
if [ -z ${RM_CMD+y} ]; then RM_CMD="trash"; fi

# List of apps. The leading br is necessary for later pattern matching
apps="$br$(flatpak list --columns=application)" || exit 1

cd ~/.var/app || exit 1

for app in *; do
	case "$apps" in
		*"$br$app$br"*) ;; # Matches if $app is in the list (installed)
		*)
			printf 'Removing app data %s\n' "${app}"
			"$RM_CMD" "./${app}"
			;;
	esac
done

(May eat your files)