Speaking as a proto-"Swicordian", I just have to say that while some sort of linear, "Legal" framework is necessary to keep the game world in some sort of casuality (but more to "justify" strategic mechanics), having those laws be overly reminiscent real-world physical laws would suck a lot of the fun escape vaule out of the game. The no-free-lunch situation could be explained in all sorts of ways that are not exaclty the laws of thermodynamics (although they have the same general gist): gods taxing magic for their own use, magic bleeding into other planes, and so on.
I don't have a particular problem with magic following magic rules. What I'm trying desperately to avoid is the "it doesn't matter, it's magic" camp getting any traction into Stardock's thinking. The laws don't need to follow reality exactly; in fact they can't if there is going to be magic involved. Siphoning energy from some sort of elemental plane clearly isn't going to follow the conventional laws of thermodynamics, but it needs to follow something that serves the same basic purpose.
More importantly, the mundane aspects of the game need to be firmly based on science. The channelers are exceptions to the rather mundane majority of the world, so the majority of the game mechanics will by necessity need to be geared toward them. Yes, the channelers are the one bring life and energy to the world, but the economy is mostly mundane. Once rehabilitated, land is farmed with mundane techniques. Mines, forges, most military training, most animal husbandry, most work on city building, etc is based on mundane technology and labor.
The basic premise of the game may be based on magic, but a huge majority of the game will be spent on mundane activities. It seems silly to not use known basic physics to describe and control these activities.