That's the thing about harmonisation of disperse markets, for every simple example of a drawback someone will come up with an example of an improvement. Regulations typically don't just magically appear, but are rather a reaction (often a knee jerk reaction) to a specific problem. Your example is good because it highlights some serious issues at both sides. For instance the increased overhead now placed on farmers, but at the same time the increased assurance placed on the customers and the government that everything is done as it should be. I.e. you know the bottle was cleaned properly before you used it, the government knows the measured quantity of goods changing hands for taxation purposes. The poor may be hard done, but they are also the ones reasonably protected.
Now this may or may not be the case here, but in a general sense this is where these ideas often come from.