I don't understand Apple's logic here. You can't reconcile the idea of "cleaning because you can redownload" with "available offline". As soon as you clean up, you are going to break offline uses.
I would guess the idea is to help enable these 500 MB per issue magazine downloads. You download a new issue, you nuke some old issue, no one cares. As long as that wasn't an issue you cared about.
I had the exact same question and your idea as to the answer is interesting. Perhaps this new behavior is in response to Newsstand's ability to automatically download new issues--users may allow those to stack up without any thought and run out of space. The question then becomes: why not just enforce this behavior for Newsstand?
Somewhat of a conspiracy theory - but if the choice for developers is risk losing losing local data or back data up to the cloud unnecessarily, I think they'll choose to store it to the cloud, as they will be the ones blamed when their app "deletes data randomly".
The more storage space taken up by local files being backed up to iCloud, the more people will end up going over their 5GB capacity, and will have to upgrade to the higher capacity plans to cover it. I'm not sure I actually believe this right now, but if they refuse to fix the problem, then I might...
I would guess the idea is to help enable these 500 MB per issue magazine downloads. You download a new issue, you nuke some old issue, no one cares. As long as that wasn't an issue you cared about.