It is possible to configure the Debugger so it does not use the default port?
No, that is not currently possible
Issue fixed in version 6.2. The latest version of Toad for DB2 can be downloaded at: https://support.quest.com/toad-for-DB2/download-new-releases
Toad has a new option to control port for communication with the z/OS Debug Session Manager. Select Options | Debugger | DB2 to change it.