Agreed - the average Default Folder X user is definitely more competent than the average Mac user (from my standpoint doing tech support, thank goodness). That's part of the reason I'm able to make a living outside the App Store - for my particular stable of apps, customers are willing and able to come find my website. There are also issues with the App Store that don't involve sandboxing, such as the fact that it's tough to build any sort of relationship with customers when we don't get any data from Apple about them, can't reply to App Store reviews, can't market or sell upgrades, etc. It makes it a lot harder to make this a long-term business instead of just a hobby.
There are exceptions, of course, and that's where things get nasty, but there's surely an optimum compromise encompassing some level of sand boxing and some level of permission management, rather than the extreme of 'everything goes' or the opposite extreme of 'no functionality'.