You say that "the colors listed are the colors at the factory stereo harness". I assume you mean the speaker wires where they plug into the head unit.
Then you say that "it is not surprising that the colors changed while getting to the liftgate". I'm not sure whose colors changed but mine did not. Or to be completely accurate, I do not remember what the color codes were at the head unit, but the factory speaker wires at the liftgate matched the referenced chart. This is, of course, just my anecdotal experience. Perhaps I just lucked out and mine is one of the few '93-'94s that match the chart. Actually, I got the chart reference from the forum where it shows up in threads now and then, so I assume that I am not the only one who has found it to be accurate.
In the final analysis, this chart (and similar ones from other sites) would be totally useless if they did not show the actual wire colors at the doors and liftgate.
I don't believe jeepdeez has actually confirmed that he has found speaker wires in the liftgate and, if so, what color they are. As you pointed out, it is difficult to misidentify the wires intended for the hatch speakers. I don't remember if mine were hidden or tied up, making them difficult to spot. I know that wiring practices for our Jeeps often changed, but mine is a very basic model and I have been amazed at the wiring harness that is included for uninstalled equipment. Even my '85 had all the speaker wiring even though I bought it new without a head unit.
Finally, I am curious what colors the FSM shows for the hatch speaker wires.