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are they implying I chemically altered the stamp?
They are not implying that you altered the stamp, but someone did.
Did you buy these from the Post Office this way? If not, someone or some thing caused the red to fade. To me it looks more like sunlight fade. As mentioned before, often the red ink fades in the sunlight a lot faster than other colors. In order for the PF to specifically say chemical exposure, they must have seen some evidence or residue of such.
This brings to mind the Copernicus stamp 1488a where the orange sun is frequently bleached out with chemicals (though while retaining full original gum). Here is an example PF certificate where they hedged the description somewhat by saying the color was removed "due to exposure to a natural or artificial source".

In other cases they have explained that they detected that the chemical alteration affected the tagging as well as bleaching the orange.

It's your money if you want to submit the entire sheet of Marilyn Monroe. It likely won't change their opinion.