The hierarchy of the question is not a big deal. He’s not trying to refute Chazal or the Nefesh Hachayim. He’s merely asking how the two can equate.
The problem is that the question takes a concept and runs with it way too far. To imply that there is no law of nature is wrong. It is likewise wrong to say that this is constantly a new world and all the items in it are replaced each instant. The idea, as expressed earlier, is merely that there is no external existence. The world depends and is made of a constant command to exist.
Rashi explains that one who recites Hallel every day is Mislotzes. He is looking fun of the lack of Nisim. This is similar to the Maharal’s explanation of the fact that there are things around that are contrary to Kvod Shamayim, and only the fact that there are rules of nature can explain this.