Edit Passbook Pass (.pkpass) file at Runtime?-Collection of common programming errors

As you already have said, Apple does not want you to create your own .pkpass files in an ios App. It is certainly possible to do so, Apple can’t NOT allow you to include or fetch certificates although they can certainly reject your app if they want to.

You can adapt code from any number of articles/tutorials to build the various files, create the signature (probably the most arcane and difficult part), and create a .pkpass file in your app. Some of the code in the signpass app is probably reusable as is, if the frameworks it relies on are in the iPhone SDK.

Perhaps you could look at some the services that are already out there that offer pass generation with a high-level API that could be consumed from the phone. This one, for example, which I present with no warranty or endorsement.