Right now the only shipping Intel MOBO's with Thunderbolt fully integrated are the expensive ASUS P8Z77-V PREMIUM, P8Z77-V PRO/THUNDERBOLT and MSI Z77A-GD80. Though on the MSI Z77A-GD80 I haven't fully read 'how' integrated the Thunderbolt is i.e. if there's any caveats.
Is there any specific reasons why the implementation of ThunderBolt hasn't gone to mainstream yet and only find on combo boards? ThunderBolt is the fastest interface now and offers a lot of potential in applications where fast data transfer are required ... like handling full HD video, audio & etc ... Why hasn't this technology implemented in Hi-End X79 boards where it is the platform most likely to be used?
It hasn't gone mainstream yet for a couple of reasons:
First, it hasn't been integrated into the chipset yet. It multiplexes a digital video signal and a PCIe signal into one stream which is then demultiplexed at each drop. This requires both a source for the digital video, and 4 second generation PCIe 2.0 lanes. Chipsets which have Intel's FDI can provide the video straight from the chipset and theoretically it could be pulled out from almost any video card that has a DisplayPort or HDMI output without much difficulty. The PCIe lanes can be tapped from the chipset itself as most have 4-8 spare lanes which are usually fanned out into 1x and 4x slots. These lanes aren't multiplexed which means they'd have to be fed into an add-in Thunderbolt controller instead of a slot on the motherboard. This cannibalizes the user's ability to use add-in PCIe cards. To better visualize this, compare the P8Z77-V PREMIUM which has Thunderbolt with the P8Z77-V Deluxe which does not.
As soon as Thunderbolt is added natively it will most likely receive its own dedicated PCIe lanes which are multiplexed on chip. This doesn't cannibalize other PCIe expansion slots and reduces the complexity of the traces on the board.
Second, Thunderbolt is really only useful for anyone who wants to daisy chain displays from FDI. On space-constrained laptops that use pass-through video (same port for onboard and discrete graphics) it may be more useful but for Desktop owners it's utterly pointless. For data there's already USB 3.0 which is almost impossible for any peripheral to saturate. With 4 USB 3.0 ports fully saturated they'd end up running into the DMI BUS bandwidth limit as well. On the desktop it's really nothing more than a solution in search of a problem.