It is now possible to get OS integration of file associations for Chrome Apps in Chrome Canary for Mac.

All you need is to enable the experimental chrome://flags/#enable-apps-file-associations flag and restart your browser.
In the screenshot below, you can see the Text App¹ is now available to open any text file. And that's because this Chrome App defined the file_handlers² key  in its manifest.

¹ https://chrome.google.com/webstore/detail/text/mmfbcljfglbokpmkimbfghdkjmjhdgbg
² https://developer.chrome.com/apps/manifest/file_handlers

Source: https://codereview.chromium.org/64803005
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