It looks like the author gave up on using Make with this commit: https://github.com/topojson/world-atlas/commit/8f92f6eb692d1...
In the package.json of that commit:
> - "description": "Roll your own TopoJSON from Natural Earth.",
> + "description": "Pre-built TopoJSON from Natural Earth.",
Based on that commit they don't need to download the data to generate the .json file, so they don't, Make became irrelevant. If anything this shows that a tool can be really useful but you don't need to marry it. Don't use if you don't have to.