My guess is that, in the world of HP:MoR, the Simulation Argument is true. Muggle science works within the boundaries of the simulation; magic operates directly on the underlying data structures, bypassing most of the Muggle-oriented interfaces by using debugging APIs. That's why it has rules that make some sort of sense, but that don't correspond to most laws of nature as Muggles understand them. Of course, the virtual machine that powers the "reality" of HP:MoR is fairly robust, which is why magic is relatively safe (i.e., you can't crash the whole of reality with a miscast Lumos), and also why magic is not all-powerful (those debugging APIs are still fairly limited).