To be honest... I haven't the slightest clue what the difference is... and I'm a native speaker... and truth be told I'm really good at my native language too. But I can tell you that "on top of" is more commonly said (I'm pretty sure). Either is fine in either instance, but to me "on top of" sounds ever so slightly more natural (I think) in most instances, so I'd just say stick with just "on top of" and you'll never raise an eyebrow. 実は、違いはぜんぜん分かりません！ でも、「on the top of」より、「on top of」の方が common (共通？）なんだと思います。二つとも結構正しいですけど、僕には「on top of」とはよりnatural soundingだと思っています。 ただ「on top of」を使えば、いつもOKでしょう。

Generally when you say " The book is on top of the table " the literal translation is that it is located Above the table. When you say that " The book is on the top of the table" the literal translation is that is that it is located above the table and Resting on the face of the table. The top becomes a location whereas just top without "the" means above. In everyday usage it means the same.