In the manual you quote, when one reads :
QuoteExtremely hot guitars can generate unwanted distortion, also indicated by a red Input LED. To prevent this,
turn down “Clean Sense” a bit.
even if clean sense is not an input trim, one may admits it's looks like strongly, with such a sentence...
Anyway, it's not the main concern :
Now with clean sense at -12dB I still got red light...Does it mean I have "unwanted distortion" I can't solve ?
No, it's red because threshold have changed in the new firmware...(And so even the manual is wrong now...)
We only ask why that change, and if it's possible to go backwards on that change because it's so confusing...