Condoms do not cover the base of the penis or any other parts of your genital skin besides the upper part of a penis. Genital warts can appear on any genital skin (buttocks, scrotum, penis, pubic area, thighs) and even in places covered by condoms. There is no requirement that only uncovered genital skin can be infected. Go see a dermatologist or a urologist for a second opinion.
See well here's the thing, I don't know if they are warts or not. I only have a suspicion that they are. They are are around 1-2 mm and in a single line on top of the circumcision scar. They really don't have a defined shape. When flaccid the skin really wrinkles and bunches in that area but if I stretch it out I can see around four slightly protruding growths.
My doctor who looked at them in June told me he thinks they are scar tissue from the circumcision. Sometimes I notice this area itching or feeling irritated from time to time so this makes me think it could be small warts.
During the encounter with the escort I was wearing a condom so as far as remember that part of my penis never made contact with her so if these are warts I am confused on how I would get warts there.
Perhaps I am just being a hypochondriac about the whole thing but maybe I should get a second opinion. What do you think?
The odds are always better that it is a recent encounter. Most warts appear after 4-6 months. I don't see the point of your question. All you can get are percentage odds and it doesn't change your health. Get it removed and biopsied to be sure or get some medical creams from your doctor and get it gone. The sooner it is gone, the sooner you can resume sex.