In nature, chemicals are found in combinations and mixtures. The companion chemicals modify the effects of each other. Isolating substances or putting them in different combinations may cause them to act very differently. Pure chemicals are very expensive. Isolates from natural materials still contain trace amounts of contaminates from their source materials.
Synthetic materials contain contaminates from the reaction process.
These impurities make the odor quality of a chemical from a natural source different than that same chemical that has been synthesized. Other properties may also be affected. In the terminology of the fragrance industry, it simply means the starting material was from a natural source rather than petroleum products. In nature no chemical is found in isolation. Relative safety of essential oils and extracts does not translate into safety of isolates and aroma chemicals.