So Normally If you want to create a shortcut in Chrome you go to Settings>More tools> Create Shortcut on the site you want and then you will have the apps shortcut but sometimes the site does not seem to have a favicon that is 128×128 pixels and ends up being all distorted. This is definitely the case for many of the Gsuite screens like the Apps page or the Admin page. As you can see below its horrible!
Anyway do not worry you can quickly sort it be creating your own Chrome extension. Following the official google guide you only need to do parts 1 and 2, downloading the example manifest.json file and editing it as needed with the right links and name. Then all you need to do is install it in chrome and your good!
I did this locally just for myself but as a Gsuite admin you can also give this to your organisation with a number of apps.
See here for examples then all you need todo is upload and install in chrome and you can have your chrome shortcut with the right logo.