Let me change an ingredient in your sentence because I'm not sure how English speakers differentiate nata from cream but those two are different from an Spanish point of view.
No puedo escoger entre el de chocolate y la torta de crema y fruta.
Notice that I've highlighted the preposition "de" that you have omitted in your English translation.
You can translate that sentence as
I can't choose between the chocolated one and the cake with cream and fruit.
where chocolated means
having or containing chocolate
As pointed by @Traveller, more naturally you can just say
I can't choose between the chocolate one and the cake with cream and fruit
The first option is not chocolate by itself, it's a dessert whose main ingredient is chocolate.
In your original sentence, the first option is the dessert made of nata - being "of" the usual English translation of "de" - where dessert made has been omitted.
No puedo escoger entre el (dulce hecho) de nata y la torta de crema y fruta.