I've had my TB display and laptop looked at and 'repaired'. The TB display had its logic board and all-in-one cable replaced, and the laptop had its I/O board replaced.
After all that, and some rigorous fault finding by myself, I think I found the source of the problem:
The MagSafe to Magsafe2 converter...
I have two of these. One for display and one for an older power pack I use. Both seemingly are faulty (what are the odds?) meaning a large portion of the time the laptop isn't actually charging / being powered. All my dealings with Apple on this have resulted in software being blamed, so this was a bit annoying.
The behaviour I'm seeing is then consistent with what is meant to happen. If the laptop loses power, the TB display switches 'off' and the laptop appears to sleep. In clamshell mode this means waking isn't possible as the only display can't be operated on battery power alone. Even if the LED on the magsafe indicates power/charging, erroneously. It seems the laptop stopped using the power when put to sleep as there was a fault, so I couldn't wake it properly... As is meant to happen.
Getting a couple of new Magsafe -> magsafe2 converters has resolved this. Perhaps try this? Or even use the power adaptor that came with the laptop instead of the all-in-one cable to see if this helps?
However, I still have experienced the issue mentioned above resulting in a hard reboot, albeit only when on battery. I think I have had two issues and confused them for one.
After all this, I am only left with the awful sound issue - when the audio circuitry switches on there is a click and an audible hiss until the circuitry switches off again with another click... But that's for another post.