Nah, that's what I was worried about too. Using the short feet on the back balances the system out and gives it (in my opinion) a better angle for typing, while still maintaining a good cenimeter or so gap for air-flow. I havn't noticed an increase in heat thus far, and I've been running her pretty much constantly since last April.
Note that I have put arctic silver on the heatsink and use Henrik's fan app when running heat-intensive programs. As it stands, she sits in her 40s most of the time, down to 27-32 when idle with the Henrik's on. If I run anything that would push her up to 55, I cut the fans on max, so she stays pretty healthy.