Is the increase in the deceased child's height and the improvement of their facial features after death considered a natural phenomenon?

What you have mentioned about your son's change of state after his death is a good sign, but matters of the Afterlife are unseen, and we cannot speak about them except with a legitimate religious proof. The age at which your son passed away places him among the people of Paradise. It has been narrated in the Hadith (definition) of the Mi'raj that the children around the Prophet of Allah, Ibrahim (peace be upon him), in Paradise are every child who died upon the fitra (innate disposition), whether Muslim or polytheist. This is in accordance with his (peace be upon him) saying: "Every child is born upon the fitra."