What about “I want to thank both you and the original article author”? Should it be “or” instead of “and”?

This seems a reach to me. I think your confusion is not unfounded and is not uncommon, but I think it's also extremely (and moreso?) common to read the sentence as the author intended. It took me 0ms to puzzle out the meaning because the intended meaning was the natural assumption of my brain.

Besides that, it seems a bit absurd to me to say that "and" and "as well as" have entirely distinct meanings. They're not totally interchangeable, but there is overlap.