When I walked the Invierno last summer, I made a point of asking people along the way about the debate over the route's "authenticity." For one thing, they told me, it's important to keep the distinction between the Jacobeo association and the church. My impression is that the church, or the arzobisprado, or whatever religious administration is in charge, is agnostic about the issue. The battle seems to be a political one -- power and dollars are at stake, and so it involves elected officials and business interests. The way has been officially marked by the government of Castilla and Leon -- there are standard granite mojones all the way from Ponferrada to Puente de Domingo Florez, where Galicia begins. From that point on, there's a wide variety of markings, much of it done by local friends associations.
If you read Spanish and are interested in the historical background, you can google Aida Menendez Camino Invierno and you will see the evidence.
But I can confirm that no one in the Pilgrim's office bats an eye at a credencial filled with stamps from the Camino de Invierno. I don't know that they have the "100 km starting point" figured out, but I don't think that's an issue for most people on this forum who will be walking it. If you start in Ponferrada, there's no question.