One wonders why they aren’t checking in the binaries for their database and language runtimes. Surely this would save crucial seconds in project setup.
Dumb false equivalence, since that ("every system library and utility it depends on") is not the argument of the side you're trying to appear to offer a response to. Please refer to the HN guidelines.
A less dishonest retort would be to ask if one should check in the dependencies that are analogous to what ends up in node_modules, and the response would be, "welp, that's exactly how many app developers have been known to approach things, so 'yes'."
I don't recognize your claim that the distinction is arbitrary. Is the NPM world's distinction between package.json's "dependencies" vs "devDependencies" arbitrary? (Answer: no.)