there ought to be a companion chip then. I was feeling the output needs to be decoupled already when thunderbolt was being released. (a damn name and a megalomaniac one, Intel could have used "zeus, the lord of olympia")
they can do a card with an I/O controller that does both video output and thunderbolt interface. there can be two thunderbolts with no problem - the PCIe 16x 2.0 or 3.0 port is a good candidate to piggyback the needed bandwith on.
triple display can be done with two thunderbolt (i.e. two minidisplayport if you don't have any TB device) and a DVI-I connector (vital for compatibility with display devices from 1987 till nowadays)
they can also sell a quadro card with six TB ports while using the same GPU chip.
here six very high resolution outputs plus six full duplex 10Gb links, on a PCIe 3.0 card!
plus daisy-chaning and basic TB graphics cards for more displays, TB sound cards with eight sound channel each, monitors, projectors, sound amps with integrated TB interface
you can build a monster contraption with a monster link to a SAN with all this.
one more application would be redirection of the final output of a bigger, high end graphics card.
here the "GF117" card will play the role of an Intel GPU in the optimus scheme, if you don't have an Intel GPU present. or if you need the outputs on its thunderbolts/displayports.