It's actually a funny story.
I used to have a Bianchi Giro and while I was in Berkley in April for a crit, it was stolen out of our team trailer. Luckily, I was able to make a claim through my parents home owners insurance and get money for it
Long story short, the shop that sponsored us had this frame on the wall for a couple years and he gave me a really good deal on it. Apparently some triathlete special ordered it a couple years back and then changed her mind. So they were stuck with this 2006 48cm Cervelo R3 which they just put on display. So I was able to get a really good deal!
The other reason why I would use a large stem and small frame is that it makes the bike a little lighter and I can get a more aggressive position. If you look at other riders like Thor Hushovd's bike he runs a 140mm 3T stem! Also, Alessandro Petacchi has a pretty long one too.
Thor Hushovd's Cervelo
Petacchi's De Rosa