From the book, there is a scene where the Elio (Timothee Chalamet’s character) removes the pit from a peach and masturbates into it. Apparently, the director Luca Guadagnino was originally unsure if he wanted to keep this scene in his adaptation. From Wikipedia:
Guadagnino was tempted to remove the scene in which Elio masturbates into a pitted peach, finding it too explicit. Chalamet was also nervous about the scene, describing it as “a metamorphosis of some of the strongest ideas in the movie” and the key to illuminating the character’s “overabundant sexual energy”. Both Guadagnino and Chalamet believed it was implausible to masturbate with a peach, but each independently tested the method. To their surprise, it worked, so Guadagnino shot the scene and ultimately included it in the film.
Never say Guadagnino and Chalamet aren’t committed to their craft.
It seems like you’re making some assumptions about what he did or did not do with the chocolate.