Actually, this is a Windows limitation...I can't speak for OSX. I rnu Mint Linux, and when I plug in a non-jailbroken iDevice, I have full access to the program folders, including Apple apps likes iBooks. I can also copy/paste files just like a thumbdrive. Here's an example: I use the app called Checkbook. It saves your registry (as in checkbook leger) as a .sql file. I use this app primarily on my iPod, but do have the app also on my iPad. I can navigate to the folder and copy that .sql freely between my devices.
That being said, I did discover a limitation. The file HAS to be copied directly from one device to the other (so both iDevices are plugged in at the same time)... My initial attempt to do this, I had copied the .sql file from the ipod to my HD, then plugged in the ipad and copied it over. This caused the app to crash when it tried to access the file. Apparently, copying to the HD changes some permissions or something. But if copied directly from device to device, works just fine.
Now, when I plug my iDevices into Windows 7, it can not see anything except photos. Yet another reason why Linux is better...