You are correct that DotNetNuke is designed to allow database objects to be part of schemas other than 'dbo', but I do believe that DotNetNuke requires that if a different schema (databaseOwner) is used, that schema must be the default for the user specified in your connection string.
So while it would be prudent to add the '{databaseOwner}' token to the SQL statements in the upgrade script files, it should not be necessary, since SQL Server will by default use the default schema specified for a user. Therefore, to fix your issue, you should ensure that the user you use in the connection string (in web.config) to allow DotNetNuke to access the database has the correct default schema specified.
If you cannot change the default schema you will have to either wait until the next version, when this token is included in the scripts, or you can introduce it your self by simply unpacking the downloaded ZIP, altering the file by adding "{databaseOwner}" in front of every usage of the "{objectQualifier}" token and repackaging it into a ZIP file. This will produce a fully-installable version of the module that should resolve your problem.
I should also note that the module has been tested in environments which use schemas other than 'dbo' without issues, but mistakes are sometimes made. If you still encounter problems, please let me know, and provide as much detail as possible (feel free to remove private data such as passwords from connection strings, etc.), by either replying to this thread or by emailing me at: andrew.nurse@dotnetnuke.com