The difference between customize function and native function in prototype

The for...in statement...

iterates over all non-Symbol, enumerable properties of an object. (source: MDN)

However, if you look at the ECMA specification, in the item "Properties of the Array Prototype Object", you'll see that:

The Array prototype object is the intrinsic object %ArrayPrototype%. The Array prototype object is an Array exotic objects and has the internal methods specified for such objects. It has a length property whose initial value is 0 and whose attributes are { [[Writable]]: true, [[Enumerable]]: false, [[Configurable]]: false }.

That applies to concat, filter, map, forEach, sort, toString etc...

You can use Object.getOwnPropertyDescriptor to check those attributes. For instance:

console.log(Object.getOwnPropertyDescriptor(Array.prototype, "concat"));

Finally, for setting those methods with {enumerable: false}, have a look at the other answer.