Does Object.keys(anObject) return anObject's prototype?

You understood the passage correctly, the usage of in here is wrong though.

It returns true, since the Array that Object.keys(anObject) returns has a property called toString in it's prototype. in also checks the prototype, while hasOwnProperty only checks the properties an Object actually has.

But it doesn't have an own property with the name toString

let anObject = {};
let keys = Object.keys(anObject);

console.log("toString" in keys); //true
console.log(keys.hasOwnProperty("toString")); //false

Object.keys(anObject) returns an array, and toString is a valid method on arrays.

Since in checks for a property in the object, and in its prototype chain, the expression "toString" in Object.keys(anObject) returns true.

But this doesn't mean that toString is an owned property of anObject. That's why anObject.hasOwnProperty("toString") returns false.