This does only apply to supplements that are considered as herbal medications. The simple fact to remove the medication term will bypass the problem I think.
It is only because they argue that medications have to be based on long tests and years of checks to call it a medication, even if most of the pharmaceutical drugs, as you said, are a lot more dangerous and less tested than what we think.
A lot of false information has spreaded over the internet about this. Even associations were created on the idea that EU will suppress all the herbal supplements, which is stupid, or they will have to forbid people to make plants growing in their gardens.