I have had a similar experience on my 67 small block. Difference being that the differences in the two small block harnesses are not as obvious as the differences you have shown. I have purchased an Alloy Metal Concours Correct harness too. I accept mine as a good usable reproduction example but I can see why you do not exactly like the one you have.
Midlife (Randy) is correct that there looks to be a black protective sleeve on two of your wires of your original harness (there is only one sleeve on mine ~oil pressure wire) while the replacement harness looks to have NO SLEEVES at all on the one you have. The sleeve on my original was more of a vinyl tube (like a heat shrink tube) while the replacement was more of a cloth braided wrapping. The connectors to the senders closer match my originals, which closely resemble your originals but not the replacement ones you show.
Yes, your harness may not be the original. That is difficult to say. I know that Ford car lines often used same and different harnesses between different models, yet often they interchanged as a whole. They just looked different in the details, like you have noted.
I couldn't help notice that your packaging label calls out as an Alloy Metals product (Revision H) and I am sure moreso now, that there were multiple vendors building these harnesses for Ford back in the day and since Alloy Metal needs to provide a "One for ALL" design, that the "revision" you have is based on a different example. It is possible that Alloy Metal manufacturer knows of a few of the variations since the "revision" is "H", which seems to indicate 8 different versions
This sounds like if you wish to match your harness EXACTLY, you would require sending out your original (or pictures of) to the manufacturer to have it custom made.