I don't think this is really true. For most important effects in large domains of physics, directly witnessing the underlying processes is as impossible as directly witnessing the history of evolution (to the extent that "directly witnessing" is even meaningful -- on a detailed level, all witnessing other than of ones own internal subjective mental states is through several layers of indirection.) We witness them indirectly, through various media whose mechanism are explained by other well-tested scientific theories.4

> If there really was a "guy in the sky" he could have absolutely made a bunch of stuff and "planted the evidence" all over the place to fool people. But if also for some reason, he always handled the laws of physics just the way things are now, we wouldn't be able to tell the difference.

IF there's really a "guy in the sky" exercising arbitrary power over the physical universe, even if he had not always handled the laws of physics in the same way, we couldn't necessarily tell the difference, since he would also have the power to make it so that our perception of evidence we examine at any given time (including our present recollection of what we might have done in the past) is always consistent with physical law always having been the same, even if it wasn't, and even if our actual observations in the past would have differed.