2560x1440 @ 24 bit (3 bytes per pixel) requires :
- 22,118,400 bytes of framebuffer (double buffered) VRAM.
- 663,552,000 bytes/sec transfer rate.
...
Multiply those values by 2. Heck, add in the requirements for the internal display (1440x900 @ 24 bit) :
- 7,776,000 bytes of framebuffer (double buffered) VRAM.
- 233,280,000 bytes/sec transfer rate.
Now you're telling me that in 2011, we don't have :
- 50 MB of VRAM (the Intel HD equipped air are configured with 384 MB)
- 12,5 Gbps transfer rate (careful, coverted to Bits per Second here, earlier used bytes) ?
Oh wait... no we don't, because Intel/Apple didn't use DP 1.2. If they did and if they made TB seperate from DP, we could use all 3 monitors on a single MBA with no problem. DP 1.2 has the bandwidth (21 Gbps vs the needed 12 Gbps) and can daisy chain. Obviously GPUs have had enough VRAM for this for years.
Yeah... no one expects a Macbook Air to drive the stuff that we could basically drive 5 years ago...

Of course, we shouldn't expect it, Apple doesn't use the proper level of specifications that exists to support this stuff.
While I totally appreciate the fact that you took the time to do a little math, VRAM isn't just about framebuffer, and it also isn't part of the equation here. The limitations on Thunderbolt display support boil down to this:
If there is no dGPU only 2 displays can be driven, because Intel's HD 3000 Graphics only has 2 DisplayPort 1.1 outputs. This is not an Apple limitation unless you consider not providing a dGPU as an Apple imposed limitation. It is right there in the specs, though, so anyone who bought one of these and is now bitter about this newfound limitation prolly shoulda read those specs.
If a Mac lacks a dGPU but has the Light Ridge Thunderbolt controller (which has 2 DisplayPort inputs), it can drive two displays off of the Thunderbolt port, but will have to blank either the built-in display (13-inch MacBook Pro) or HDMI connected display (Mac mini).
The MacBook Air uses the Eagle Ridge Thunderbolt controller, which only has one DisplayPort input, and thus can only drive 1 external display. I'm guessing this decision was based on the smaller size, power consumption and cost of the Eagle Ridge chip. What's interesting is that Apple provides a full Light Ridge chip in the mini, which also has a very small form factor and carries a lower retail price to boot.
Every Thunderbolt equipped Mac with a dGPU comes with the Light Ridge controller, and can thus drive two displays connected via Thunderbolt as well as any built in displays or HDMI connected displays. If you're talking about a 27-inch iMac with two ports, both displays can be conventional DisplayPort 1.1a panels because no daisy-chaining of displays is required.
Thunderbolt does not support DisplayPort 1.2 or Multi Stream Transport. This is also not an Apple limitation, nor would it be trivial to add support for these features. A DP 1.1a main link + aux channel can carry a maximum of 8.641 Gbps of data. This will fit on a single 10 Gbps Thunderbolt channel. DP 1.2 requires 18 Gbps for main link + aux. This would have required a single Thunderbolt channel to provide 20 Gbps of bandwidth. If they stuck with the full-duplex, dual-channel architecture, Intel would have had to come up with a cable and connector that could support simultaneous, bi-directional 40 Gbps throughput. We're just not there yet, I'm afraid, and it doesn't look like Cactus Ridge is going to get us there either.
The other thing that's not here yet are any devices that support DisplayPort 1.2's MST, despite the standard being released in the final days of 2009. If I'm wrong in saying this, please correct me, because I thought the technology sounded great when it was announced.
As you pointed out though, solutions to drive 2 or 3 external displays off of a single DisplayPort 1.1 stream have existed for some time, and are totally feasible for use with Thunderbolt Macs. This would allow simultaneous use of 3 external displays plus the built in on the MBA, or 6 external plus the built-in on the 27-inch iMac. Granted, these solutions only work with lower resolution displays, e.g. 2@1920x1080 or 3@1280x1024.
The oddest limitation the original article brings to light is the lack of ability to chain a DP display directly off an ATD, but instead having to put another device in between. I can't conceive of why the ATD doesn't support DisplayPort compatibility mode signaling, aside from the logical suggestions made earlier that this could easily lead to unsupported configurations and thus was intentionally disabled by Apple. This is annoying if it can't be worked around aside from adding at least $100 worth of nonexistent Thunderbolt dongle or even pricier devices in order to continue the chain.
I'd also like to add that Apple's suggestion to make the ATD the first device in the chain provides two obvious advantages. 1) The first hop in a chain has the lowest latency, which could help the quality of the video signal in certain situations. 2) You don't accidentally lose your display signal if you power down or disconnect an intermediate device.
My guess is Apple used dp1.1 just to get TB out in time for 2011 models.
They want to cut costs, so next major update will be 2012 and they needed something to boost sales of 2011 model.
Of course the consumer looses, first half of that year went without any TB products.
Once again, if Apple had chosen to put TB in usb socket, they wouldn't have crippled the dp port.
But maybe it would have been too complicated "for the rest of us" to still plug 3 cables to new shiny (reflecting) apple display...
But now the damage is done, and Apple is too bold to admit they chose wrong and change their product lines fast. We will be stucked for years in a situation where 2 the most bandwidth hungry pipes are tied together and both suffer and then we have these additional legacy ports having very little traffic...
Once again, go ahead and show me a DisplayPort device that requires DP 1.2 or uses MST, or a consumer electronics cable that carries more than 20 Gbps, full-duplex.
Lowly, crippled DisplayPort 1.1a provides more video bandwidth than either Dual Link DVI or HDMI 1.4a, so therefore the ThunderBolt ports on Macs are actually more compact and capable than the vast majority of video out ports built into devices shipping today.