Yes, the final say is always on the particular custom where the goods will get the clearance, so they will call the shots on the way the procedure should be done.

The IT system in place is just there to accommodate how customs should proceed, so if they have different ways to solve the problem, the customs officer will just find the one he's more used to.

But you're right that if there's a HSCode for something built, furniture vs wood for example, then the more "accurate" should be used, as they will have different tariffs too.