To me, the reasoning seems to be:

Npm, pnpm, and yarn are written in JS, so they have to use Node.js facilities, which are based on libuv, which isn't optimal in this case.

Bun is written in Zig, so it doesn't need libuv, and can so it's own thing.

Obviously, someone could write a Node.js package manager in C/C++ as a native module to do the same, but that's not what npm, pnpm, and yarn did.