Great question. When we initially built the atom snap it was just easier to ingest the deb to make the snap. Snapcraft is super flexible in this regard, being able to ingest build artifacts from elsewhere in the release process. So rather than re-build it, we went for making a snap from the deb.
If someone wanted to have a go at building from source, and make a pull request against the snapcrafters repo, we would certainly take a look, but doing that work isn’t critical so nobody on our team has taken the time to do it yet.
We had hoped that we could hand the snap over to the upstream developers, rather than have the snapcrafters repo responsible for building the snap. Unfortunately the upstream developers were not interested in taking this on.