Using SQLServer 2012 Enterprise, I don't see "Package Configuration Wizard" in SSIS when I do a right click in Control Flow tab. I can see all the other items (Log, Digital Signing...).
Here are info about my install:
Microsoft Visual Studio 2010
Version 10.0.40219.1 SP1Rel
Microsoft .NET Framework
Version 4.0.30319 SP1Rel
Professional
SQL Server Analysis Services
Concepteur Microsoft SQL Server Analysis Services
Version 11.0.2100.60
SQL Server Integration Services
Concepteur Microsoft SQL Server Integration Services
Version 11.0.2100.60
SQL Server Reporting Services
Concepteurs Microsoft SQL Server Reporting Services
Version 11.0.2100.60
It is still available, but hidden because configuring a package is a little different in the 2012 Project Deployment Model. But if you open a package, right-click in the Control Flow tab, click on the Properties of the package, then you will find a Configurations property under Misc.