I think I have solved the issue and it doesn’t seem to be related to the zipping process as I first assumed.
It turns out that the packaging process in the UXP Developer Tool modifies the manifest file. In my source manifest file, the host entry is an array of objects containing only the PS app object. In the packaged ccx, host only contains the PS app object, not an array.
After changing my source manifest file to match this, everything else works as expected.
I figured I’d share the fix in case anyone else encounters something similar.
I found the solution from this thread: http://forums.creativeclouddeveloper.com/t/marketplace-submission-manifest-issues/2073