If I understood correctly, you wish to know why free fatty acids (FFA) are low in an oil sample while FAMEs content is high. The raw oil contains quite low quantity of FFA (0.3-3.3% source: https://www.sciencedirect.com/topics/food-science/free-fatty-acids) while remaining fatty acids are present as triacylglyceride (TAG-bound). During trans-esterification reaction, all these fatty acids (FFA + TAG bound) gets converted to FAME leading to high fatty acid profile as compared to the lower FFA content in the raw oil.
Refer this for your analysis of FFA and TAG bound FAs: https://academic.oup.com/chromsci/article/50/10/934/344702