Scarcity and uniqueness can also drive premiums. There are plenty of absolutely wonderful fine flavor cocoas out there that have amazing flavor profiles that people would (and do) pay premiums for. One of the Asian submissions this year to the aforementioned competition tasted like caramalized pears - now, i've been in cocoa for a long time, and this is the first time I've seen a cocoa that tasted like that. It's one of the reasons I've stayed in it, no matter how much one knows, it seems in cocoa there's always something new to experience and learn!
Most regions are heterozygous collections of multiple clonal varieties to begin with, primarily a function of their disease resistance, productivity, or just dumb blind happenstance with not much thought given to why that particular tree was planted. There are many, many clones to choose from, and numerous ways to approach planting materials - you can plant a new tree, you can side graft, you can shoot graft, etc. Your planting material absolutely, unequivocally influences the flavors you can get from your cocoa. Where it's grown and the agronomics at play also can have a huge impact on your flavors (soil nutrition, composition, elevation, climactics, etc). As I'm sure you're aware, by altering the fermentation and drying conditions, you can get a 100 different flavors from the same beans, so obviously there's much that can be done here as well.
Oftentimes, cocoa buyers are buying from 4000 miles away, and may rarely have 'boots on the ground' to know exactly what's occurring, regardless of what they think they're buying and what they think is happening 8-) Hence I'm guessing why you reference your experience in Papua. There are lots of reasons a corporation may have for identifying specific locations, of which flavor may be only one element.
Interestingly, on the wine - I enjoy wine. I'd say given my work in chocolate, my taster is a bit more developed than your average person. Last year, I had the experience of having a $25,000 bottle of wine. Now, it was good, to be sure, but I'm not sure it was that much better than a $50 bottle - I've had some pretty darn good $50 bottles. It could be that for me, in wine, my taster isn't sufficiently developed to appreciate that level of sophistication; if that's the case, the wine is $24,950 too expensive for me - there may be those out there who experience the same wine very, very differently than i do, and appreciate it much more - for them, the price may be justified. I find that to be the case for me with cocoa quite often - i 'see' things in cocoa that others simply don't pick up on, just because I've been doing it for so long and I'm so familiar with it. Generally speaking, those cocoa's that I love the most, I find that the general population has very little interest in, as they're too different from what they've come to expect as 'chocolate' as defined by their mainstream experiences.
However, it could also be that the wine's really meant to be a $50 bottle, and what we're seeing here is the power of marketing. Either way, the fact someone bought it reflects there's a value proposition there, be it on the merits of the intrinsic properties of the wine (it's flavor), or the extrinsics (marketing panache)