The version number you set while creating the package (in the PackageMaker Project) is the version of the installer, not the version of your .app-File. It is needed, so that another installer can see if he downgrades the current installation or not. The installer will never ever look at the contents it is installing to the system.
To set the version of your your .app-Bundle, right-click your .app-file and select "Show Package Contents" from the appearing menu. Open the folder "Contents", there you will find a file called "Info.plist". You have to edit this file and have to set your version-info for your application there. You can do this by using Property List Editor (included in the Apple Developer Tools) or another tool like BBEdit for example.
To read from your .plist in your application, you need a special library. I recommend the Java property list library from Daniel Dreibrodt (more information about the .plist-Format you'll find in this post on my blog).
Generelly, you should set the version-info of your app-bundle, anyway you use it for updating-purposes or not. If it is not set, the user has no chance to get information about the version he has installed without launching your software.
What you need is not the version of your .pkg file, you need the version of your .app-Bundle. Anyway - the version of your .pkg-file is handled the same way as your .app-file. There is also the Info.plist, where you find the informations. It can also be parsed with the same library.