Defending Pantheism

[Belacqua]

The sense of the numinous (or holy) is more directly related to the inner emotional attitude of the pantheist and has little to do with what the universe actually is. But the pantheist's pronouncement of the numinosity of the real world is more than mere fiat.

It might make sense to sort of bracket this question and come back at the end of the thread. If I'm understanding you right, you may be saying that pantheism is "everything that exists is holy," whereas just plain non-religion would be "everything just exists." The latter position differing only in that it doesn't see things as holy. 
So if pantheism could be argued for persuasively, then the holiness would take care of itself. 

If you hold the view that "some things are valuable or spiritual above and beyond common, local, contingent values" you must ask "What kind of force is responsible for the existence of such transcendent values?" If one is a theist, the answer is easy: God (the immaterial, spiritual kind who likes to write on stone tablets). 

I'm not sure about the word "force" here. Lots of Christians hold that there is a God but that it's not a "force" in that it's something imposing values on us. The Platonic Christians, for example. And my main guy, Blake, who elaborately argued that anything or anyone who imposes values or laws upon us is definitely not God. Quite the opposite. 
So probably we aren't able to oppose only two -isms: God as arbitrarily handing down laws, vs. pantheism. Probably you don't mean to make this dichotomy, but I want to be sure that Christian views of God are often more subtle than a big guy who writes on stone tablets. 

The pantheists answer is: they come from nature. And if nature is the source of these transcendent values, nature itself is a holy/numinous thing

Oh, well, there's your definition. That which we call holy is that which gives us our values, if they are transcendent values. 

I don't think that quite matches the Google definition, but it might be usable. 

Like atheists, pantheists believe that the best way to understand the universe is through logical inquiry and scientific investigation. THOSE are the ways to figure out what the universe (or God) really is. 

That may be so, but I think we're not there yet. There are a number of other steps needed, surely, to get to the above statement. 

Because I don't think anything about pantheism per se says that logical inquiry and science are the only ways to know things. In pantheism, everything that really exists is God, including stuff we have no idea about. What about this rules out non-logical or non-scientific ways of understanding? People are limited, including in our epistemological theories. We may not know everything about epistemology. Though we are a part of everything that exists (and therefore part of the pantheistic God), there is no necessary reason to assume that our current beliefs concerning ways of understanding is all that's possible. 

Unless you're beginning with the definition that nature always and only equals the stuff that human logic and science can examine, and that only this particular kind of nature exists. That may be so. Or it may be that there is all kinds of really existing stuff in the universe which neither human logic nor science can ever get a handle on. Or it may be that in rare cases people have other ways of knowing. Does pantheism per se come down one way or another on this question? I don't want to beg the question and assume that the nature which pantheism calls holy is only that which people know in the two ways you specify. 

And I'm not suggesting we should believe in anything supernatural, since neither the word "supernatural" nor even the word "nature" is easily definable. I'm just saying that we aren't justified yet in assuming that "all the stuff that really exists," whether or not it equals a pantheistic God, can only be known by those two means. That's how it's worked for us, apparently, so far; but that's not proof.