I got my new 13" Retina in the other day (late 2013 model ME865LL/A)
I was all excited to see if the two Thunderbolt 2 outputs and the HDMI output would work together, but plugging in the HDMI output knocked out one of the Thunderbolt outputs, so what I read was right, the 13" model will only power two external monitors. Before I got this I kept reading over and over how it wasn't possible, but that was dealing with the Late '12 or the Early '13 models, I was hoping that the upgraded video card on the newest Haswell versions may be different, but alas, not to be....
But I did implement a work around as I have a Matrox Triple Head 2 Go DP Edition for my old Macbook and what that does is make my two Lenovo 22" widescreens look like one big 3840x1200 monitor to it's host (tricking the MB to thinking "hey, this is one monitor"), so this allows me to use one Thunderbolt output to power these two monitors and then I am using an HDMI --> DVI cable to power an HP 23" widescreen monitor I also have running at full resolution, all this in addition to the Laptop display as well:
Here is a quick 20 second video of all monitors playing video.... the one on the left in the middle row was staggering but that is more a problem with AMC's website more than anything, I never get good stream speeds from their site
https://www.youtube.com/watch?v=OfIsupl3psc
I just installed iStat 4 an hour ago and am showing CPU temps around 150 degrees, not really sure what "normal" is or what is acceptable...... I'm going to keep tabs on what the temps are as I finish up my workday here (another 6 hours to go)
I still want to re-arrangle things so i only have two levels of screens to deal with, but still formulating that setup with my desk