Incorrect. You have not provided any documentation that states differently from Intel's official information release.
The difference it seems, is how that information is being interpreted (not as clear as it could be).
That is false information. I suggest you research how LightPeak and Thunderbolt differ to prevent you from making a fool of yourself any further.
Since you think they're two totally different technologies, why not post the sources (particularly on LightPeak) that you're getting this impression.
Incorrect. Thunderbolt alone is based from PCIe. Light Peak used its own protocol.
Think about this logically for a second. PCIe on it's own cannot handle daisy chaining of devices (must use a switch to have multiple end-points, and each of those end-points has it's own wiring to the switch - not over the same wiring). So they had to make some modifications, which will include the protocol (what the TB chip actually does).
In light of this, the differences aren't as stark as you may think. In fact, the only difference, is that they didn't include the optical transceivers.
Now if I had to guess, the optical cables didn't work out to be a cheap as they initially expected and/or were going to be delayed (which haven't arrived yet). Personally, I expect both issues occurred. So they made the change to get a product shipped (they want their R&D money back + a lot more

). It's also cheaper for system vendors this way, and in the case of laptops, makes it a bit easier, as there's less complexity and more importantly, less PCB real estate consumption as a result.
TB can be included on PCI-E video cards because it will have direct connection to PCI-e data lanes and the graphics processor.
This is one possibility. But not the only way it could be done as mentioned previously.
Now whether when/if Intel will go for this isn't clear, but it's in their best interest IMO that they do settle on a method due to users' desire to share peripherals with more than just laptops (or AIO's) that come with TB ports.
They have a 12 month "lead time".
A lead time isn't the same as exclusivity (they're willing to sell to other vendors, but so far, none of the others have a product ready yet).
Apple accomplished this by working with Intel and the other developers from the beginning on the software end. What's happening now, is the pay-off. It's allowed them to beat the competition to market by getting their hardware (MBP with a TB chip) and software done earlier than anyone else.
Incorrect. The MBP is simply the first product with it. If it had been released on the MP, you'd probably say "Thunderbolt seems to be aimed at desktops" instead.
Maybe. TB doesn't really offer much to the desktop market alone though, and wouldn't generate as much interest for adoption.
Users with desktops equipped with PCIe lanes can do better with existing solutions (separate GPU card + RAID storage systems can out-perform what TB can do; even with a Promise R6).
For laptops OTOH, it offers a significant advantage than what's previously been available for most (faster connection than they've ever had before, and potentially fewer wires to boot).