Thank you very much for your reply. I will be looking back into our installation to see if we can diagnose our issue.
So the behavior for xowiki file upload you describe with a-c is working correctly. The issue still remains that the link generated for the file does not link to anything in the CR which leads me to your #2.
We are also experiencing excessive storage usage (x2 - x4 > expected) w/in the CR (folders appear to be recursively copying), which I think might be related and confirms #2.