Thanks for the post. The HPV DNA test approved for clinical use, the Hybrid Capture 2 HPV test, is only approved for use with the cervix specifically. It isn't used as a general means of checking one's HPV status, or with external genital warts.
Genital warts are usually diagnosed clinically with a visual inpspection and you're right, sometimes there can be confusion. Getting a second opinion is not a bad idea if the diagnosis is unclear, and sometimes a health care provider can use a magnifying lens to help with the diagnosis. It would be good to see the new doctor while the lesions are still there, if possible.
If in fact you do have genital warts, that only means that so many others, you've been exposed to a common skin virus; up to 75-80% of sexually active people are thought to contract HPV at some point, although for most they never are diagnosed.
Some experts believe that removing genital warts may lower the risk of transmission since it reduces the areas of tissue that contain most of the virus. Removing warts cannot guarantee that the risk of transmission is removed. However, if no symptoms recur in the subsequent months following treatment, the chance of transmission dramatically decreases, and some researchers consider the possibility of being contagious during this time would be minimal to remote.
I hope this helps but if you have other questions, post anytime.
All the best,