Here is some documentation.

http://support.apple.com/kb/HT5219?viewlocale=en_US&locale=en_US#dispnum

Specifically this, noting the footnotes. I've done some editing for readability:

How many Apple Thunderbolt Displays can I use with my Mac in OS X?

The table below indicates how many Thunderbolt displays can be connected to Thunderbolt-capable Mac computers in OS X.

Computer Maximum number of connected displays Thunderbolt-capable Macs with only Intel HD Graphics 3000 integrated graphics can support one connected Apple Thunderbolt Display (27-inch):

MacBook Air (Mid 2011), MacBook Pro (13-inch, Early 2011) and (13-inch, Late 2011), Mac mini (Mid 2011), 2.3 GHz, Mac mini with Lion Server (Mid 2011)

Thunderbolt-capable Macs that can support up to two connected Apple Thunderbolt Displays.

MacBook Pro (Retina, Mid 2012), MacBook Pro (13-inch, Mid 2012), MacBook Pro (15-inch and 17-inch, Early 2011) and later, MacBook Air (Mid 2012), iMac (Mid 2011), Mac mini (Mid 2011), 2.5 GHz,

Note: The F8 key does not work when using Windows with a USB keyboard connected to an Apple Thunderbolt Display (27-inch).

1 You can connect a second Apple Thunderbolt Display (27-inch) to a MacBook Pro (13-inch, Early 2011) and (13-inch, Late 2011), but the built-in display on the MacBook Pro will go dark. This is expected behavior.

2 iMac (27-inch, Mid 2011) with two Thunderbolt ports supports a total of two Thunderbolt displays regardless of which Thunderbolt port each display is connected to.

3 Mac mini with AMD graphics can support an HDMI compatible device on its HDMI port when using two Thunderbolt displays.

4 MacBook Pro (Retina, Mid 2012) can support an HDMI-compatible device on its HDMI port while also using two Thunderbolt displays.

And here's an OWC article with an image showing a MacBook Pro with Retina that has three attached displays plus the built-in.

http://blog.macsales.com/14241-macbook-pro-15-with-retina-display-can-run-3-external-displays

It's likely that the external display connections are simply wired directly to the discrete GPU. The internal display is connected to a gmux chip that handles switching between GPUs and it probably would have been significantly more complex to route the 3 external ports the same way.

I think it's fair to assume that most users connecting external displays will have AC power available, so this seems like a fine way to simplify things.

It's definitely not an issue of graphical power - I use an external 2560x1440 monitor with the new Iris Pro-only 15" rMBP and previously used it with an Intel HD 3000-equipped 13" MBP, both of which handle it fine.