that a molecule of l-dopa is the same as any other molecule of l-dopa whether it was extracted from a plant or made in a flask. Often, natural extracts can contain impurites that may or may not give you undesired side effects. The chemically pure substance made via synthesis, is actually better because it's checked by the FDA for quality before it is allowed to be marketed, also the bean extract has no carbidopa in it so more of the l-dopa content is metabolized (decarboxylated) to dopamine (that doesn't cross the blood-brain barrier, so it is wasted) before it reaches the brain. When you have high blood levels of dopamine outside the brain, then the likelihood of side effects (on the heart mostly, but dopamine in the peripheral nervous system can be responsible for dyskinesias).
Like rev pointed out, we are ALL DIFFERENT in our ability to gain symptomatic relief from l-dopa. This is due to many factors, some of which are still unknown.