Some folks raised eyebrows when I told them that one of my aways was HSS, so there is something to that theory. To combat against that, I would make sure that my other away(s) diversified the picture (different region of the country, perceived lack of prestige, etc.). My other aways were at Emory and Rush and this lent credibility to the (true) position that I just wanted a big city. Also, I had a free place to stay in all 3 places, so that was convenient. Now, the other common theme is that each program is the best one in its respective city, but I didn't bring that up.
As far as harvard v. penn, I have heard (never been there) that aways at harvard are a waste of time b/c you just stand there and watch and people ignore you. Like I said, I've never been there so I don't know how true that is.
I did interview at Penn and liked the place a lot. The people were nice and the facilities were AWESOME. Also, philly is WAY better than boston in my opinon.
I would base your decision on which of the 2 you would rather be at instead of how other folks may perceive your choice. If somebody gives you a hard time, explain your choice in terms of personal factors (geography, family, schedule conflict, etc.).
-Grizzle-