Answer
We find evidence of an endomembrane system based on the structure of the system. The areas of the cell where vesicles travel would the the endomembrane system. There is no proof that vesicles travel and merge with mitochondria or chloroplasts. Also, the parts of the endomembrane system are a single membrane whereas mitochondria and chloroplasts are double membranes.
Work Step by Step
Don't confuse the endomembrane system with the endosymbiont theory which states that mitochondria and chloroplasts appear to have once been unicellular prokaryotic cells that were engulfed by eukaryotes and now this larger cell is what we call a eukaryote today that has multiple organelles. See page 109, section "The Evolutionary Origins of Mitochondria and Chloroplasts." Also, for more about endomembrane system see page 104, concept 6.4.
