First off I'm not a doctor just someone who had a virus,
HPV, that tried to kill me so I have tried to learn as much about it as I can.
I personally didn't have any pain associated with my
HPV related SCC, either in my Primary which was the BOT or my 2 affected nodes.
Just because you tested positive for
HPV (I assume cervically) doesn't mean it traveled to your tonsil region. There has not been any evidence to suggest that it travels throughout the body but there is evidence that it must be transmitted by contact from body region to another body region.
I also believe that even though the tonsils were removed it is possible for the
HPV to infect the Squamous cells remaining in that region including the Pillars.
Re the biopsy, I would probably push for it.