I found out how to customize the Chrome web site tile icons now too!
To create the web site app tiles in the first place, go read posts 617-619 in the today thread: Today  - Page 62 - Windows 10 Forums
After they are created open file explorer too C:\Program Files (x86)\Google\Chrome\Application\48.0.2564.103\VisualElements, be sure to use the current Chrome version number. Then paste the same PNG icon you used to create your Chrome tile(for an example see: Solved Windows 10 Themes created by Ten Forums members - Page 131 - Windows 10 Forums)
You will need rename the original icons by adding a number at the end of the name(easier to remember original name) then paste your new tile icon in and give it the name "logo", then paste the icon again in and name it "smalllogo"
the folder should now look like this:
Now when you pin your site "apps" to the start menu, they will look like this:
You might want to save the two new tile icons somewhere for when Chrome upgrades, as I am not yet sure if they carry over(I doubt they will though) as I just figured out how to do this: