Two questions in this thread:
Managed PCs. There is currently not a workaround for this, but we are working on this as a top priority. Can you please submit a support incident at www.adobe.com/support/digitaleditions/?
My Documents on another drive: This has been tested rather extensively and works. The only issues we saw were where the My Documents was mapped to some kinds of network drives, or where the user simply moved their My Documents folder without using the OS' tool (i.e. right-click on your My Documents folder and select "Properties", then change the target in the dialog using the Move... button. Does either of these fit your case?