Revisiting the GitHub Actions Release system (.flatpak + .deb) by Stefterv · Pull Request #1204 · processing/processing4
This is not how --install-deps-from works.
You'll need to
commandLine(
"flatpak",
"remote-add",
"--user",
"--if-not-exists",
"flathub",
"https://flathub.org/repo/flathub.flatpakrepo"
)first and then --install-deps-from=flathub.