Some passages in the MN read like apologetic excuses. He writes about certain unpopular ideas, mentioned by a variety of Chachomim, that they are Daas Yachid although you don’t find any Amorah actually arguing the idea.
This shows us in which vein it is written.
So, it is an interesting Sefer. I’ve read parts of it but not all, I think. But it is not supposed to be the basis of our outlook of what the Torah is. Nor do the philosophical proofs help a non-philosophically oriented generation come to the same conclusion.