If Thunderbolt is a successor to DisplayPort, why can't it support DisplayPort multi-streaming?
You should be able to and it may be a limitation of the system you are on or any intermediary devices.

Here's my setup:  Dell Precision M3800 with nvidia Quadro K1100m graphics.  Connected out of the Thunderbolt port (by a mDisplay port cable) to a Dell U3014 monitor which is connected to another U3014 (by a full size Display port cable).  I had to enable DP1.2 on the monitor in the settings for it to work.

I'm looking to see if I can use the Elgato Thunderbolt 2 Dock in between my laptop and the first display to utilize Network, USB, etc... in addition to dual displays.