I was doing a comparison between 3.5 and 5.0 and noticed that the repackager does not provide the ability to use a template when it is importing the ".inc" file.
The Legacy Conversion Wizard in 3.5 had the ability to specify another MSI as a template. But it looks like in 5.0 the Legacy Conversion Wizard was was removed and its functionality added in the repackager.
In 3.5 we I using templates as a way to standardize my packages and so that I can pre-configure some of the common settings.