In my experience, most apps on the Chrome store are what Google calls "Hosted Apps": a link plus metadata and an icon [0]. They also provide "Packaged Apps" [1], which are downloaded and run locally as you describe, but this style appears to be much less popular with developers.
Being hosted doesn't make them just links. Hosted apps still have access to many APIs not available in normal web pages. Such as cross-domain XHR, background pages (apps can run in the background even when the tab is closed), a licensing API that allows Google to handle the registration burden, etc.
I think I see the source of our disagreement. You seem to say that Chrome's impressive infrastructure for web apps gives it a potential advantage. I certainly agree with that, but the capabilities of Chrome apps aren't widely used right now, so the actual strength of the system is still unknown. The Chrome Web Store could still end up like WebOS: great platform, few developers.
I don't agree with the article that Firefox is in trouble, but I'm a Chrome Store dev and I've grown tired of reading people online saying things like "they're just bookmarks", so I apologize if I came across as attacking. I think the advantages that Chrome (and to a lesser extent IE) has will eventually be rolled into the spec, and will be negated, however I don't think Mozilla is doing enough to push their alternative as viable. Their spec, to me, reads as web app best practices and the only original thing they're providing is an install button api.