Of course, you can create your own MCUXpresso project and integrate the Embedded Wizard Build Environment source codes and the generated code by yourself.
The provided template project (and the PostProcess) are just for convenience in order to allow the user to play with the different GUI examples.
You can create your own MCUXpresso project (and name it according your needs), then you can add the folders:
/Application/GeneratedCode
/Application/Source
/PlatformPackage/<colorformat> (please take care that you are using the color format that correspond to the color format used in your Embedded Wizard GUI project)
/PlatformPackage/RTE
/TargetSpecific
... (SDK, your drivers, ...)
As soon as you are using your own MCUXpresso project, there is no need to use the PostProcess (and it will no more work).
I hope this helps.
Best regards,
Manfred.