There are no formal industry standards as to what "single-origin" means. It's probably not a bad idea because of the widespread use of the term and the potential for misleading buyers.
I stopped using the phrase "single-origin" when talking about chocolate a long time ago because, for me, it's no longer either meaningful nor helpful. I now just use the single word "origin." An origin chocolate is one where the place where the beans come from is indicated on the label.
The origin may be big - an entire country: Venzuela. It could be a region: Carenero, Sur del Lago (by Lake Maracaibo), Ocumare. It could be small: a village/community (Chuao) or a farm (Hacienda Concepcion, Hacienda San Jose).
Is a chocolate a single-origin chocolate if it is a blend of beans from two different growing areas of the same country?It might be if your definition of the origin is an entire country. Otherwise not.
Another nuance to consider for companies adding cocoa butter to their chocolate: To be a "true" single origin the cocoa butter has to come from the same place that the beans come from. It's not single-origin if the beans are grown in Venezuela and the cocoa butter is Ghanaian deodorized.
If you really wanted to be picky about it, a "true" single origin would have ALL of the ingredients come from the same origin. Should a "single-origin" from the Dominican Republicbe made with Dominican sugar?
Finally,a varietal name is not an originand can be confusing. Ocumare is also a varietal - and they grow in other places besides Ocumare. (I've seen them in a gene bank in Bolivia - at least they were identified as Ocumare, but that's another story.)
In the end, you have to trust everyone in the supply chain to be telling the truth. Traceability is supposed to be part of agri- and social certifications. Does that mean that accidents and fraud don't happen? Of course not.
Sebastian is totally right about genetic variability within a pod. It depends, from what I have been told, on how many times the flower has been successfully fertilized. This more times, the greater the genetic diversity within the pod. From what I have been told, cacao is nearly unique, if not unique in this respect.
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clay - http://www.thechocolatelife.com/clay/