Regarding the comma usage I agree with Junkseller's point of view. I can add to that with once I took a writing class and we use to do a writing exercise. It simply was whenever a new thought occurred to end the last with a comma and not pay attention to creating paragraphs.
It was when edited that sentence structure took place while creating the parenthetical. Ultimately as writers we seek to convey a message. That can be a short thought process or one of length. Adding too I at times use . . . for a long pause before a new thought.
Also, a good point to ponder is the audience. For me my muse comes to mind when writing. I know . . . I know that may be thought of as archaic. But, to whom is the writing actually focused? That is somewhat singular in form though not of format.
What is interesting to me is we as readers with emphasis as writers tend to have a lean of editing as we read. That may be somewhat innate or natural. I know for me I at times lose the meaning of a writing when I change things in my mind. I lose the intent of the author.
I can fathom a guess with the meaning of the thoughts shared with the quote as I see it. Firstly, I consider order and structure of clauses . . .
A complete system is the subject focused on moral and spiritual order
Contrast/compare meanings as philosophical 'or' religious being of difference
Instead of 'I mean to say' I insert 'perhaps'. Next as I interpret with meaning is 'its weight as truth (Alluded to being religious or philosophical) followed with having 'doubt(s)' while is not reliant upon reasoning (Cognitive thought) or inspiration (Intuitiveness) or from a reliable source. In other words it just is as is . . . is so.
The middle ages relied on religious authority before the age of enlightenment when philosophy spurted with difference between the rational and experiential seeking justification for knowledge as a truth be that existence, reality, or God.
There was contrast with a priori and a posteriori justifications while Kant's view with those synthesized is at task too. There is inference to the ontological and with tautology or the author is very familiar with formal philosophy. He is very familiar with the theology of that era as well. I would look to Thomas Aquinas for support for the reasoning of a marriage of those two as one.
He concludes IMHO that no matter all the preceding what arrives simply arrives while from where is of no consequence since it is . . . as is . . . is so.