If it can be found in nature (in ANY amounts) it should be good to go. As you alluded to in your vitamin C example, it would be impractical to gather enough DMAA from the plants alone to produce commercially. The lab setting just permits a more efficient means of extracting the active from the plants to produce in greater amounts commercially. IIRC I read that the FDA had doctored the results of a study about the presence of DMAA in the geranium plant. Supposedly they changed the verbiage from there being "a detectable amount in parts per billion, to 0 detectable parts per million". While this may be an valid statement, there were still quantifiable amounts of DMAA in the more sensitive test. If I'm mistaken, please feel free to correct me a I've been out of the DMAA litigation loop the past few weeks.
edit: So to address your question about how is it different? Well one is a water soluble vitamin, and the other is a potent stimulant that has a similar chemical structure as an amphetamine.