Which operating system did you test against to?
Have you try on Windows 7?
What if you create a SSIS project, for example, flat file conversion and load to db first, then you convert to Project Deployment Model?
There are many cases, but your answer may be only one of them.
I tested on Windows 7 Enterprise, using SQL 2012 Developer Edition, and Visual Studio 2010 Team Suite also installed. I started on SSIS new project for flat file conversion and load, then converted it to SSIS Project Deployment Model, i could see both .ispac and .dtsx files within /bin/Development folder. Please note that .ispac file only created when you create the project with Project Development Model, or first time you convert your project to Project Development Model. Later on, the build for the project only create .dtsx file, no more .ispac file.