In Admin Center, the new Zendesk branded logo supersedes any custom favicon/color you use for your account, as far as I can tell. I could be wrong, but havent made it work. 

This is a problem in admin center, because the interfaces between production and sandbox are identical, aside from the URL being different. It makes it risky to move quickly. 

It would be cool if you could pick a different color for the admin center Zendesk logo, if you wanted to for your sandbox accounts. Obviously, using the favicon would be nice in general that is configured in Zendesk, but this could be a happy interim solution.