It's _mostly_ talking about the speed of the surrounding tools. They wrote a package manager that speaks NPM (presumably in C++ or zig instead of JS) which unsurprisingly completely dominates NPM in performance.
The other stuff he benches is built into the runtime ... HTTP requests, copying files, and a webserver Bun ships with. Presumably the Bun team wrote these tools with performance in mind, but the article doesn't compare features. I'm skeptical the webserver in particular is at feature parity with the ones he benched against, which makes the numbers look pretty watery to me.
It does not address the runtimes of JavaScriptCore (Webkit/Bun) vs V8 (node/deno) which, as you pointed out, are probably very similar.