EU countries are closer now to US states than to independent sovereign entities when it comes to the movement of goods and people. This is by design, not by accident and there is nothing naive about it, it's a founding principle of the EU.
There are zero customs checks between states in the EU customs union, because that’s literally what “a customs union” means.
If you don’t like the EU or don’t want to be a part of it, that’s your opinion and yours to say, but what it is includes a customs union.
The real issue is that the EU is coming up with extremely naive regulations that put the burden of cost and effort on citizens and inefficient local governments to enforce them. If they really want these substances to be disposed of safely, they have to make it free for corporations and individuals to hand them over to a government agency and fund this with taxes.