Here is the situation:
I own a Google Apps for Business account.
I have two domain names registered :
I think the real answer is to be found in Google's Limitations for multiple domains:
"Custom URLs for accessing Google Apps are available only for the primary domain. The Admin console enables the administrator to set a custom URL for various services. The custom URL applies only for users accessing the services at the primary domain. The same limitation applies to custom web address mapping for a Google Site."
It's quite a severe limitation, since it requires you to open a new Google Apps account for each custom domain you want to register, even if all domains belong to the same organisation.