No, it actually doesn’t. In thermodynamics (and physics generally I think) we focus on the system - interconversions between forms of energy, how much goes in and out, etc., but we treat the surroundings as essentially a black box without detailed knowledge. We don’t care where the surroundings got it’s energy, we just call it a thermal bath (a theoretically infinite source of energy) and move on to our calculations on the system.
No, we just acknowledge (as we already do, regardless of God) that those laws only truly apply to isolated/closed systems.
Let’s take the 2nd Law of Thermodynamics as an example. When I was young I was told by YEC folks that it was a defeater of evolution – the law says that entropy never decreases for spontaneous processes, how could complex life then form spontaneously from less complex life? The law is violated!
Except they were forgetting the precise language and limitations of the law. The law says in an isolated system the entropy never decreases spontaneously. And here we see why complex life on Earth is not a violation of the 2nd Law of Thermodynamics – the system (the biochemical reactions, or even the Earth itself could be defined as the system) is not an isolated system and so it can lower it’s entropy by increasing the entropy in the surroundings. For us to conclude that life doesn’t violated the 2nd Law we don’t need to know anything about the nature of those surroundings (which would be the rest entire universe, so we have no hope of knowing it exhaustively) other than transfer can occur.
I think this is important: as long as God is part of the surroundings and not the system (which is what methodological naturalism provides), then I don’t see any violation of the laws of physics for God to provide an external force or energy sink/source. The system is the thing we are studying, investigating, measuring, etc. but the surroundings we don’t have much knowledge of at all (usually just things like whether mass and energy can flow freely to/from it and whether it is hotter or colder than the system).
On the other hand, seeing an external force of energy sink/source does not mean God, it could be an “ordinary” physical source that we just didn’t know about. I mean this is the how we get things like black holes and dark energy. There is something out there that seems to be providing extra energy to the universe, but we don’t actually know what it is. I don’t think we suddenly say all the laws are violated.