"MS SQL Disk Space Quota" resource usage shown at Home > All Resource Usage in CCP is bigger than the actual usage shown for the hosted database within the subscription at More Services > Databases >
The MS SQL disk space usage is calculated for all hosted databases, which includes MS SQL system DBs. Logging in to the Web Data Administrator of the subscription and listing the databases, the total size will consist of the database hosted by user and 'master', 'msdb', 'tempdb' databases, stored by MS SQL service.
Per the documentation, available at http://download.automation.odin.com/pa/6.0/doc/portal/6.0/oa/51566.htm: The size of all databases including transaction logs is limited by the new Disk Space Quota resource.
"All databases" here means precisely that all possible space occupied by MS SQL service is accounted.