ideviceinstaller workflow: Problems with archiving/reinstallation

I'm currently playing around with the up-to-date libimobiledevice and ideviceinstaller on Linux connecting to a redsn0w jailbroken iPhone 3G iOS 4.2.1

Having a fresh ipa file of any app I can install it using "ideviceinstaller -i ARCHIVE". Then the application is used and some user data is stored. When the app is archived (via "-a APPID" app+user data) and restored at a later point in time ("-r APPID") the full state of the app including user data is restored.
When making a copy of the archive to the connected PC I assume that the file being restored with the -r option is copied unmodified to the PC. When opening it, one can see Payload (=app) and Container (=user data) subdirectories. Trying to use this archive for a reinstallation from the PC fails with the error "Unable to locate Payload folder in archive!".
To my investigation the reason for that is, that the archive coming from the device does not contain the directory entry for "Payload" itself, but the archive listing ("unzip -lv") looks like

0 Stored 0 0% 10-13-2012 22:41 00000000 Payload/<appname>.app/
6700 Defl:N 6705 -0% 10-13-2012 22:40 3f2ff0eb Payload/<appname>.app/<filename>

In contrast to that the original ipa files lists like

0 Stored 0 0% 09-24-2012 22:07 00000000 Payload/
0 Stored 0 0% 10-18-2012 00:28 00000000 Payload/<appname>.app/
737 Stored 737 0% 09-24-2012 22:04 6736c91f Payload/<appname>.app/<filename>

Repacking the file ("zip -r *" in the extracted directory) on the PC yields a zip file which gives a listing similar to the original one with the subdirectories listed (and which is btw much smaller because the phone does no compressing). This one can be processed with "-i ARCHIVE" option. I don't know if this is an artefact of jailbreaking or if the archives are generally missing these directory entries when they are created on the phone.

Additionally there is no user data available after installation from an archive containing app and user data, only the app is installed like using the original archive. So either the behaviour of the installation process is incomplete or there is an option for a complete restore as it is done with archives sitting on the device itself is missing. Currently it is contra intuitive that one can archive apps together with user data, but there is no (direct) way of reinstalling them completely.