Water from a pond and tap water are both heterogeneous mixtures of things dissolved and suspended in H2O, they are in fact very different. A synthesized chemical will be identical to the same chemical produced in a plant. The synthetic counterpart will just be in a mixture with distilled water or a neutral food grade oil.

It’s a better analogy than you think. “Petroleum” is very much a hydrocarbon “pond water”.

How confident can you be that the end result is filtered appropriately, every time?

Its not filtered, its the result of chemical reactions and purification steps and you can measure the result. Same reason why your tap water is safe, the resulting product, either water or a purified chemical has impurities monitored by a variety of analytical techniques.