There is certainly a problem here. It is kind of like having two marriage ceremonies with two different brides. There needs to be a choice. Just like some countries don't allow dual-citizenship, you can't be confirmed as a Catholic if you don't intend to live as a Catholic but instead have allegiance to some non-Catholic authority and hold non-Catholic doctrine.
While there is much we hold in common with the Lutheran church, such as the fundamentals of salvation/justification, we have many differences, not least of which is ecclesiastical authority and the Papacy.
If your son believes the Catholic Church to be the seat of authority, as established by Christ, in Peter and the Apostles, there is no reason he shouldn't see the Catholic Church as his true home.
It is not elitist to suggest that one church holds the fullness of the faith, and only the Catholic Church can make this case which goes far beyond what I have just said.
I would suggest you meet with your priest and talk more about it, in detail, so you can more fully grasp the inherent contradiction of affirming two disparate doctrines.