There's no way it was only €3,200. They would've spent way more than that on just fuel for the engine testing plus the man hours, cost of the engines, analysis, etc... Are you sure it wasn't €32,000? Even that sounds low.
It's right. VW fees are about 1.300-3.500€ for typical approvals.
It works in different way. Big cost is from homologators, they are big base oil producers and additive producers (or both). Approval is commercial permission only, big boys make the chemistry and rest buy base oils and that chemistry to sell it.