The limitation is that EG 4.1 doesn't tolerate folders with identical paths among different repositories. Because EG presents this as one aggregate view of everything -- it does not merge folder contents that originate in different repositories.
For example:
FOUNDATION\BIP Tree\Report Studio\Reports\Stored Processes
HR\BIP Tree\Report Studio\Reports\Stored Processes
Would create a conflict -- ONLY IF EG is pointed at the HR repository, which "looks through" to Foundation.
Chris