Very interesting. I see no reason that a waste heat capture system couldn't be used, so long as it doesn't create any restriction in the exhaust.
IMO any restriction there would cause soot/fouling issues, and those already seem kind of prevalent in the chinese diesel heaters. I've always wanted to ceramic coat or line the combustion chamber in one of these, as I feel that doing so could allow the chamber to maintain it's heat better and then burn cleaner. If you enable a way to make the combustion not such a sensitive process, It would become more complete and I feel it wouldn't be so sensitive to a device in the exhaust, like a muffler or this egr cooler.
Also, if you're going to do something like this, use a coolant/water that doesn't contain silicates, as the high heat will cause them to precipitate in the cooler much like they would if installed and used on an engine.