We really don't see these issues with pure Thunderbolt products... and the certification and testing requirements don't even allow for any wiggle room when it comes to having a Thunderbolt product approved. The issues seem limited to displays and in the case of the Thunderbolt display, however the video is handed off such that it is with an external mini-Displayport to video cable and with the same kinds of issues.
I agree interference or a signal failure/degradtion or timing with the video chipset/memory/shared memory is already shown to be different factors with this OR it's actually noise from the Thunderbolt/video into the system that is the factor. A specific die rev of memory appears to be a factor (not necessary true cause / but subject to cause) in Mac mini systems. In multiple systems, Mac minis - MacBooks - iMacs, have seen issue resolved with the replacement of cheap MDP adapters in the case of non-thunderbolt displays...
Of course - when you have a Thunderbolt Display from Apple, with integrated cable - the situation is more difficult to remedy, especially if other things can adjust/control do not rememdy. In the case of MacBook Air and Retina models with this issue occuring, the only other factor to adjust would be what else is connected to the actual system of the Thunderbolt display.
With those thoughts shared.... I'd summarize / suggest - Thunderbolt itself isn't the issue here. The issue is manifesting with connected displays, the Thunderbolt display included (which at some point has a handoff from TB to the video output as noted above) - and as the issue with 3rd party DVI/HDMI displays has most often been resolved with a better/proper quality cable, very well may be a deficiency that Apple can resolve in a future Thunderbolt display design to fix the issue there as well. Either that - or it's a sensitivy in the video chipset.
As I continue to walk through this... can also note - significant improvements / reductions of this issue over the last 12 months have come from various Apple EFI and OS updates too. Perhaps more to come there too.