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I do not know the exact rationale of the Alire devs, but Ada already uses (since 83) the word "package" to indicate a module or namespace, so calling dependencies a "crate" seems to avoid confusion with an Ada "package".
The crates of the community index [1] are somewhat vetted because they are added to the index using a PR on GitHub. You're not required to use these external crates though, you can create your own monorepo if you want.
My personal experience has been that a package manager (for any language) makes it much easier to download and build some project.
[1] https://github.com/alire-project/alire-index
The GNAT toolchain that Alire installs automatically is built by GitHub Actions runners from the GNAT-FSF-builds [1] repository.
You can download the toolchain as a tarball from the releases page and use it separately if you'd like. If you use Alire, it'll take care of downloading and unpacking the tarball and add it to your PATH when called via alr build.
[1] https://github.com/alire-project/GNAT-FSF-builds