The following PKs and FKs don't appear to use the objectQualifier during installation:
DocumentSettings.PK_DocumentsSettings
DocumentSettings.FK_DocumentsSettings_Modules
EventLog.PK_EventLogMaster
To reproduce, start with a fresh install and update the "objectQualifier" value in the release.config and web.config files to be some string (let's say "foo"). Run the install and then look at the structure of foo_DocumentSettings and foo_EventLog, you'll notice that their PKs and FKs aren't named PK_<objectQualifier>_<keyName>.
This made it difficult to perform a second installation on the same SqlServer database. I've renamed the values and will be trying to install another instance of DNN momentarily. If I missed something I'll post again.
Thought you might like to know about this.