I still don't understand why you want to compile Godot instead of just using the one we ship in the build containers. But if you want to do so, see abmyii's build script (https://gitlab.com/abmyii/ubports-godot/-/blob/v3.4.0-ubports/build-ubports.sh) which he runs without Clickable, but within a clickable container (https://gitlab.com/abmyii/ubports-godot/-/blob/v3.4.0-ubports/.gitlab-ci.yml).
If you are just interested in cross compiling with Clickable in general, that is pretty straight forward. The build containers are set up in a way that you only need to tell Clickable which architecture to build for and Clickable chooses the according prepared build container. If you are interested how they are set up, see the Dockerfile: https://gitlab.com/clickable/clickable-docker-images/-/blob/master/ubuntu-sdk/16.04-cross-build/Dockerfile.
And finally, if you want to compile dependencies along with you app, see this guide: https://docs.ubports.com/en/latest/appdev/guides/dependencies.html