Can the HD 4000 of the Macbook Pro Retina 13 easily handle 2 monitor at 1920x1080 or would it be better to buy a Macbook Pro Retina 15 because it has a separate GPU ? At the Macbook Retina's release, I heard it had some scrolling issues because of the large resolution it had to deal with and I do not want to experience that on external displays.
I plan to plug the 2 monitors on the 2 thunderbolt ports.
Although I have not used it first hand, I would not expect you to have performance issues running the two extra displays. The main retina display is actually drawing 4 times as many pixels as the external displays, and then scaling the image down, so a Thunderbolt display is not going to make much of a difference.