Much of what NGO's do ends up being neutral or even harmful because they think in 3 year funding cycle timelines, and they say what funders want to hear to get their capital. it takes a cacao tree 3 years to produce, 4 to produce to nearly full capacity, so farmers and ngo's have fundamentally different time perspectives. to get funding they typically say something like "we will expand production from 150 to 400 Ha., form and strengthen associations and co-ops, assisting 500 families, provide tech assistance from crop management through post harvest, and help with marketing so they can export at fine and flavor prices, plus organic and fair trade." in other words, impossible to do in 5-7 years, much less in 2 or 3.
i have run a non-profit before and know many people in that industry, they are nearly 100% good people with fine intentions, but this structural problem in how they attract capital and the length of their programs often ends up convincing farmers to invest in nonsensical things. like, as you say, cert.'s and business practices that are not sustainable when the outside $$ go away. And, as a businessman, i would say that the ngo folks are usually not businesspeople and when they get involved in marketing and logistics its not their strength.
As for USAID, they have lots of $$ and a mandate, and within the limits of that mandate i think they do a good job here in peru. I have said to them many times that some small % of the $$ should go to prevention in areas that are not yet coca producing, not just to increasing hectarage of cacao in current coca areas. but like all govt. programs they do their best within strict guidelines, and they're good people, not like the caricature of bureaucrats.
In my area the average association would be 50-60 producers, maybe? some as many as 300+, some as small as a dozen farmers in one caserio.
post-harvest is interesting. my project buys beans en baba, or with the pulp on, strictly separated by variety, and we do all the post-harvest, and export into the fine market. farmers here love the model because most of them are coffee farmers as well, and right as the cacao harvest is heavy the coffee ripens and they have no time to attend to their cacao. in my model, they spend 2 days a month on cacao, make more $$, and have more time for coffee. in my area, most farmers just want to be rid of post-harvest. but that may not be true in other areas, you would know better. also, other than my project, there is no sales option here that gives a premium for quality, so any time spent on fermentation is time lost.
which is the long way of saying that there isn't a clamor for post-harvest training here, but that may be a local phenomenon. if full fermenting and complete drying during the rainy season paid well and didn't cost high value time away from coffee i'm sure they would do it.