I figured out Amazon Software License does not restrict us from distributing the source and added the missing submodules, ec2-ami-tools and ec2-api-tools. Now the source is exactly the same to what git.vyatta.com has.
Also, remember I said submodule paths are now correct? I lied. Turns out I forgot to push that. Now they are correct, you can verify it yourself: https://github.com/vyos/build-iso/commit/e9c10e908b2d441132d5ddb46f26e7af668f84e4
To check I didn’t do anything wrong I cloned the source myself to a clean machine, initialized all submodules with a for-loop and built some. It worked. Let me know if it doesn’t work for you.
Now I need to build all submodules and produce an ISO from them to verify clean build without the use of precompiled packages works.