That makes no sense on either point!
> The cover and that things that go on it are as much a part of the book as any other page.
Indeed, and a book should not be judged by any single page alone. Not the cover, nor page 39.
> This saying is so outdated and comes from a time when all book covers were essentially the same.
If all covers were the same, there would be no temptation to judge the book by it, and thus no reason to invent a saying cautioning against it, so I doubt this history.