2D, this is really a very important point, i.e. whether intra-Schengenland flights must land at customs airports. I have always understood that this is not the case, as you confirm.
However as reported above this could become a matter of controversy with local officials.
The solution would be to carry in the aircraft some quotation from the relevant legislation to present as evidence in such circumstances.
If 2D or someone could post here a link or suchlike to the relevant chapter and verse, this would be a service to all ppruners!
Incidentally I have come across an alleged exception to the general principle for intra-Schengenland flights, Denmark apparently requires flights to (say) Germany to depart from regulated airfields. Maybe someone can confirm this.