Erroneous Commas?

I think the difference is that, in the second sentence, the phrase or joining word is used in apposition. Where the first sentence includes a compound direct object (as you correctly identified), the second sentence has a single object (conjunction) in the prepositional phrase, and that object is further elaborated with the appositive or joining word.

Thus, it's grammatically correct, technically. Admittedly, however, this is confusing usage. If I were the author, I would have used parentheses for the appositive to avoid confusion:

Don't automatically place a comma in front of every conjunction (joining word).

"Don't automatically place a comma in front of every conjunction, or joining word."

This looks like irony to me. The author is humorously breaking the rule in the very sentence warning against it. Is this author given to humour in the rest of the piece?