Apple Thunderbolt Display-Connection confusion!

OK, I have quite a lot to explain here so this is going to be a big post.
In September, I'll be going to University to study Computer Games Animation and as such over the past few months I've sorted out the computer I need for the course, or I thought I did anyway. I intended to buy a Mac Pro (the upcoming model, following the rumours of an early August update for 2011) and two Apple 27" Cinema Displays. Along with this, I was going to purchase the Atlona HD620 (on one side of the device there is an MDp output and HDMI output to put in your Mac and 360 into and the other side is another MDp output to your display) to connect my Xbox 360 to one of the displays (MDp). I was aware that the HD620 doesn't work with the 2011 iMac due to Thunderbolt and thus it was possible I would run into the same problem with the new Mac Pro and displays. I kept my plan however and decided I'd look into it when the time came.
....and then it did.
Yesterday as I'm sure you're aware, Apple went and released the new Thunderbolt Display which did away with MDp completely. I looked into the new displays and Thunderbolt and as I now understand it, Thunderbolt is backwards compatible with MDp but obviously, MDp can't be forward compatible with Thunderbolt. In other words you can insert a Thunderbolt input cable into a MDp output but you can't insert a MDp input cable into a Thunderbolt output (right?). This would make sense regarding the HD620 and the new iMac as the iMac only possesses a Thunderbolt output forcing you to input Mdp from the HD60 into the Thunderbolt and thus, doesn't work.
This however is not the case with the Thunderbolt display. As I'm sure you're also aware, the Thunderbolt display possesses an output AND the built-in Thunderbolt cable. Now I wonder if using the Thunderbolt cable into the MDp output on the HD620 would work? The HD620 would then be connected to the Mac Pro via the Apple Thunderbolt cable from the (highly presumed) Thunderbolt output on the Mac Pro into the MDp output on the other side of the device and I'm hoping this would work. I'm also wondering, despite using Thunderbolt cables between the Mac Pro and the display, even if this does work, would the MDp element on the HD620 cancel out the USB outputs, speakers, FaceTime camera and mic functionalities on the display?
I hope this makes some sense, I've been rattling my brain over this for months and as much as I love the new displays, it's a real pain that they've come out now and shaken my plans. I hope there are members here who know what they're talking about a lot more than I do on the subject, my understanding here could be completely mistaken. Infact the more I think about it and the more I learn, the less confident I become. If this isn't right, is there any way this set up could work?
Thank you.

I'm in the same predicament.  I'm making a series of purchase decisions, and unfortunately some are on hold until I can arrive to a solid conclusion.  To give you some insight, I had the MacBook air with the MDp and just switched to a MacBook Air with the Thunderbolt primarily because I have a iMac 27" w/ Thunderbolt at the office i wanted to use as a external monitor.
With that said, I'm still waiting to decide on what to buy for the home to extend the MacBook Air as I have four choices:
- Cinema Display 27" w/ Mini DisplayPort
- Thunderbolt Display 27"
- iMac 27" with Thunderbolt (similar to office) (used in target display mode from time to time)
- iMac 27" with Mini DisplayPort (used in target display mode from time to time)
The burning question is, how do you plan to use the display and then determine if compatibility exists in those methods.  In my case, I plan to use the display from OSX as well as Windows via Bootcamp.  It turns out, through relentless research with a visit to the Apple store and purchases, I arrived to the colusions here:
http://mike952.wordpress.com/2011/07/21/thunderbold-and-minidisplay-mac-compatib ility-101/
It seems Mini DisplayPort works all around, meaning I can reboot and the display works even prior to the OSX loading, in BootCamp, etc.  This lends credulence that the DisplayPort monitor will work with any DisplayPort device be it an XBox 360 or your latest cable box, whatever.
With thunderbolt, it seems as though the two end points need to be thunderbolt as they need to negotiate with each other and agree on how to transfer the video stream.  This is validated somewhat with my bootcamp partition on my iMac 27" at work.  When I boot into bootcamp, I cannot get the iMac27" to work in target display mode via the thunderbolt to thunderbolt with either mini displayport or thunderbolt cables. This is also documented on Apple support.  However, Bootcamp does work fine with an iMac27" with Mini displayport and the thunderbolt MacBook via a mini display port cable (not a thunderbolt cable).
So the conclusion I've arrived thus far is the Cinema Display w/ Mini DisplayPort plug is more compatible with Mini Display or ThunderBolt sources (equally) however, it require the use of an additional USB connector to activate the isight camera and usb ports on the back while the Thunderbolt display, nice to have one plug enable all the features such as USB, isight camera, etc. however may not work with external displayport devices without some future adaptor or firmware updates with
With the iMac 27" thunderbolt, the devices need to be synchronized via thunderbolt in order to achieve the target display mode (meaning, they need to be on, macbook needs to be open to use the Command + F2) and there after you can close the MacBook to use the iMac 27" as the monitor.
With the newly released ThunderBolt display, and this is where I'm curious and wish Apple will step in and answer so I can make my purchase decision now, the question is will this display auto-synchronize with thunderbolt source (a requirement for it to work seamlessly when plugged in) and if so, this means their must be some software/hardware running in the monitor to accomplish this.  Is this sync still broken when booting to BootCamp?
In other words, will BootCamp work with the thunderbolt display despite it not working with the iMac27" in target display mode?
As a software engineer, I'm inclined to say there are a few possible solutions here:
- firmware option to use thunderbolt port as a mini displayport and operating systems see it as so allowing for interoperability skipping the thunderbolt negotiation step
- bootcamp update allowing Windows to work with thunderbolt port similar to mac, allowing for negotation and the invokation of Command + F2 on iMac 27" and presumably auto negotiation and display iwth the Thunderbolt Display 27"
- some inteligent thunderbolt powered adapter which, when plugged in, tricks any device into seeing a mini displayport monitor and allowing it to function as so be it the iMac 27" in target dispaly mode OR the Thunderbolt display operating simply as a former cinema display.  Whoever comes up with this adapter will be a millionair over night.

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