Chrome Web Apps don't get a separate dock icon in Gnome 3. A way around this is to use Epiphany for web apps, but the downside is that all links will open in a new Epiphany window.
How can I have Epiphany Web App links to open in Chrome?
what chromium does atm is just to find the browser desktop file, and use it as template for its webapps, by doing:
- "Exec=" => updated to run the browser with the --app= flag
- "Name=" => updated to match the webapp title
- "GenericName", "Comment", "#" => dropped
- "MimeType=" => dropped
- "Icon=" => updated to use the site's favicon
- everything else => copied vanilla.
Thus if you found these files and made GNOME Shell recognize them, you should also find their icons/starters in GNOME Shell's Application Menu (if that's what you're after, i.e. I didn't misunderstand your question).
This method will allow you to add separate dock icon in Gnome 3 for chrome web apps https://support.google.com/chrome/answer/95710?hl=en