Hi there. I'm the owner that originally did Yakima rack install (see here: http://www.fordedgeforum.com/index.php?/topic/1890-yakima-q-towers-and-bamr/).
I can tell you that it did not scrape the paint, even after repeated installs/removals. The clips have a soft rubbery coating and the clips exert much of their pressure evenly across the flat surfaces on both the clips and the body surfaces. There have been no issues. Read the thread and you'll find many Q & A.
Enjoy your Edges, folks !