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It looks like rust to me. I used to have a couple rust spots on the A-pillar also in my '01 ES (as a result of paint being chipped; we all know Lexus paint chips easily compared to other vehicles), so I cleaned and lightly sanded the rust out, and touched it up with the Autovisuals paint pen. It looks great
Unfortunately it's hard to tell from just that picture (whether the rust is coming from paint peel, bubbling in the paint, etc.), but then again no picture will do it justice; seeing it with my own eyes is no comparison
Try to send a PM to "Guitarman", who moderates the CL Detailing forum. He's an excellent resource for this kind of question.