Problem is that what you say is not what I see in the article. The article feels like it describes differences between plugins and standalone application IN GENERAL, not from the perspective of "how good/bad can those be handled by the current architecture of appstore, etc.". So yes, I might have missed this point... since I couldn't recognize the point in the article.
Regarding handling applications in appstore - what exactly should be that problematic? Downloading is the same, changes notification is the same as well... Okay, in such case some unified installer would be handy, what is the problem with that? Some pre-configured "installer template" which installs all applications to a same place (similarly to plugins), puts Start menu links in the same place, etc. Of course that "same place" where the applications would be installed would need to be added to PATH, so that one can run the application from anywhere (as one would expect), etc. I don't see that as a showstopper... but I admit that I may be well missing something since designing such architectures is not my primary job.