Salam
According to the Gospels of Ahlulbayt (a) (words of Isa in form of Injeel handed to Mohammad (s) and taught portion of by Imams (a)), the word "son" is akin to what Quran describes as "Muqarab". Close (one) to God.
A Portion of the Gospel | Jesus through Shiite Narrations | Al-Islam.org (see the 5th narration for the long Gospel of Auli-Mohammad (S)).
The Quran sometimes shows in a general meaning, all believers have proximity to God, same with the Tanakh, sometimes believers all can be "sons of God". Sometimes its the close ones to God from Angels, and hence refers to them.
Sometimes in Quran, though, the close ones to God means the best of the best, mainly Prophets and their successors. Women wise its Sarah, Mariam, etc, people chosen and exalted and nearer to God then other believers.
So you have "the only proximate to/son of God", this means the one who is the door to God and exalted way above all others at that time. Isa (a) was at that time when he was a Messenger, the only exalted one. John died. Elijah came back but was hidden.
Remember the thread about oneness of God and Isa (a). He says Jews are taking his statements out of context, he shows "sons of God" in general meaning (believers wise), and so is saying, the context gives the meaning.
The verse with "Janballah" would literally mean God has an upper leg part, the thigh. In reality it means "the one right beside God", or God's closest one, and is about the proximity of two bows/arches or closer still, and according to Imam Ali (a) it refers to the station of the Imam of the time. So perhaps, "the only son..." had a meaning of something more akin to this.