First of all, there is absolutely no reason to build Godot yourself. Simply pick a build from our spine-godot documentation:
Secondly, there's no "official" way to do Godot engine modules. We need to keep it outside the Godot source tree so we can actually have it snuggly sitting in our spine-runtimes repository, without having to pull in all of Godot as well.
This is a common thing for 3rd party modules, and I posit that it's the only sane way to do it. There's a reason the Godot build system has the
custom_modules flag which allows you to pull in directories outside the Godot source tree.
We've written extensive documentation on how to compile Godot with the spine-godot runtime yourself, if you absolutely need to do that (you don't, download it from our site):
If you still want to compile things yourself, you will also have to compile export templates for the platforms you support. That's a major pain, as you need to setup build infra for those platforms. E.g. you can not cross-compile for macOS and iOS from Windows or Linux. We've thus also provided a GitHub workflow, which lets you build everything on GitHub, using their build runners for all operating systems. This is also documented in the documentation.