What is the maximal thickness for choux pastry?
This is not necessarily under baked.

What you made is a perfect creme puff. The dough in the middle is not raw- it has just been steamed from the inside instead of being dried and crisped the way the exterior was. There is usually very little such dough on the inside and the filling hides it.  

Many creme puff recipes call for scooping out the soft dough from the middle before filling.

I don't know that there is any size that can guarantee that there will be no un-crisped dough left in the middle. Even medium-sized eclairs can have a few threads of dough inside that stay soft.