Your two thoughts seem to contradict, but in the spirit of the article, they actually reinforce one another. Chesterton is correct that there is “no reason” apple trees shouldn’t produce iPods ... and yet they do not. They produce apples, and we can clearly observe the mechanism by which they do this, every time.
In the same way, we must affirm, if we’re faithful to Scripture, that the universe is sustained in its existence each moment by God. However, at the same time, we can study the laws of physics by which this occurs.
Now on the other hand, your second example starts from our capacity for observing and describing reality (what we call “science”). I hadn’t thought of the mold example, but in many other Levitical regulations, we can also see the practical benefit: avoiding carrion-eaters, washing regularly, laws of sexual purity that maximize the chance of conception.
However, the “good science” part of this doesn’t take away from the spiritual reality: that holiness, the observance of Halakha, is an end, rather than a means of earthly betterment.
(Did that make sense at all? I have to go to Walmart now ...)
I’m going to defer comment until you come back from Walmart. I always like to pencil in a few moments from time to time where I actually think.