Based solely on your quotations, I would use the following analogy:

Suppose you like to buy and sell bags full of chocolate eggs. You know from past experience that roughly 10% of the foil-wrapped eggs are spoiled, but the only way of knowing which 10% of the foil-wrapped eggs is to cut them all open, which would be uneconomical and destroy the entire value of the product.

So maybe FedEx knew that P(illegal|pharmacy) was greater than P(illegal), but that P(illegal|pharmacy) was still too low compared to P(pharmacy) to justify shutting down all pharmacies.