Well, I continue to be baffled.
After running about 40 miles in 4 hot/cold cycles, I took a 3 oz sample of atf and did the soldering iron trick...no water.
Did it twice to make sure!
So, I am going to flush the cooling system a couple more times with distilled water and will watch carefully for any change to the coolant or atf.
I have continued to watch the half-gallon sample of the offending coolant. It has maintained its burnt orange color and has not phase separated in almost a week. This tells me the color is not coming from atf.
I hate to admit this...but the only explanation I can come up with is when I flushed and switched over from Toyota red three years ago, I must have "missed" some. IIRC, I did about 4 distilled water flushes and then topped off with Prestone all makes/models. Then last year I drained the system and re-filled with the same coolant. It looked fine then as I recall.
It wasn't until just last week I noticed the color change. And I am under my hoods several times per week on average (yes, I am a loser!).
Even my best answer is not very good...I really have a hard time believing some residual Toyota red took 3 years to start discoloring my Prestone and making some goo.
I don't know what else to say....