Another take on the word “so”: In 5.210 of CMOS, “Interjections and functional variations”: “… most parts of speech may be used as interjections. A word that is classified as some other part of speech but used with the force of an interjection is called an exclamatory noun, exclamatory adjective, and so forth.” And the word “so” is used as an example of one of these “exclamatory” words.
Specifically in regard to the word “so,” I think this interpretation opens a can of worms. If the word “so” can now be an interjection, it must take a comma after it. You must now decide each time “so” is used what the speaker is thinking and whether or not “so” is a conjunction that means “therefore” or it is an interjection, a throwaway-type word, and has no meaning. As a conjunction, “so” does not have a separating comma after it; as an interjection, it does.
Inserting the comma for the interjection does not shed light or clarity on the sentence and forces the person punctuating to intuit what the speaker is thinking or, at the very least, to look back at what is said before the word “so” in order to try to figure it out.
Interesting! We’ll talk more.