I think you have underscored the difference here. I said in a previous post that panentheism does not seek to provide an answer to the puzzle, which is yet another form of dualism and dialectical thought with a thesis, antithesis, and a synthesis. You are trying to "explain" omnipresence scientifically, that everything is of one "substance"; a sort of spiritual reductionism, if you will.
What I like about panentheism is that it allows for differentiation and non-differentiation or fusion, simultaneously. It's not "All is One", to the exclusion of "All is Many'. It is rather like this, "From the One to the Many, from the Many to the One". Again, nonduality does not exclude, whereas monism does.
I don't believe panentheism says that spirit is "in" everything. To quote from Buddhist thought, "Form is emptiness, and emptiness is form. Form is not other than emptiness, emptiness is not other than form." There is both uniqueness, 100%, and sameness, 100%. It's like the Christian doctrine of the Hypostatic Union. In the truest sense it is Mystery, or Paradox, as another word. It is self-contradictory. You can't have 200% of a single thing. Transcendence and immanence, not 50/50, nor 0/100, but 100/100. Like the Trinity, 1+1+1=1