Exactly how it impacts it I am not sure of, I just know that we had problems in a similar setup, and our portal developer eventually found out that there were some known issues with federated portals. That was three years ago, so I had some hopes that SAP had fixed those issues now.
The problem we ran into was that depending on the address we set up for the link we either:
1) Got a link that took the user into the UWL in the existing portal (web browser) window, but it was the UWL of the local portal which was not connected to any systems and thus would always be emptry
or
2) Got a link that opened a new web browser window every time a/the link was clicked (a user interface problem), and I can't recall now if they also would have to navigate to the UWL. Too long ago for full details from my memory unfortunately.