Webstores basically allow Google, Apple and others to monetize discovery for users that don't know better.
Many people have a seriously difficult time comprehending the concept of a URL. In fact, most of the time if you give some technologically illiterate people a URL, they will not enter it in the browser address bar, but instead type the URL into Google. Google will then give results for something like www.mydomain.com and people will click through to that site.
It is entirely conceivable that Google eventually puts links to it's Chrome webstore apps as sponsored links in the future, once this happens, users who look for your site through Google should find two links for you, one sponsored via the Chrome store and one unsponsored which is the actual link to your site.
If you use the Chrome store for monetization, you ostensibly give up margin to Google. For this reason I would put a free app to my site in the Chrome appstore and monetize people directly on my site. To do otherwise would mean giving up margins unnecessarily to Google.
Of course, this doesn't happen now. But I imagine that it is only a matter of time until Chrome AppStore results show up as sponsored links in Google web search.
On the otherhand, it's possible that Google only sponsor results for paid apps only.