Making chocolate in small batches doesn't have anything to do directly with making a better chocolate bar.I agree with most of your points (both in this post and more generally elsewhere on the site), and even acknowledge that you might be right if you define "directly" in a particular way. But I'm almost certain you haven't made your own small-batch chocolate, and would guess you haven't personally compared products from the producers being discussed.
You are right that small batch doesn't matter much, but timing is crucial. Freshly made chocolate has a lot of volatile flavors that dissipate quickly. Large producers age their product to produce a consistent (and sometimes excellent) product. Some small producers achieve a much faster turn-around from roasting to consumption.
I've both made chocolate and done a lot of comparison, and I've never tasted a mass produced chocolate where the taste is comparable to a fresh batch made by an amateur using quality ingredients. I suppose that theoretically it could be done, but in practice, to my taste, freshness has always had the flavor advantage.
My usual comparison would be coffee: freshly roasted and freshly brewed coffee tastes significantly different than freeze dried. Both have their place, but you should doubt the taste of anyone who says there is no significant difference. Fresh versus canned tomatoes is another example I've considered. There are some excellent canned tomatoes, and some lousy fresh tomatoes, but no canned tomato is a decent substitute for an excellent fresh tomato.