first of all, have you really been diagnosed by an expert?
Sometimes 1-2 very small wart-like bumps could be other things and not always genital warts. Me, for example, have been diagnosed having genital warts june last year and ever since i've ever had 2-3 similar situations with very small genital warts (which turned out to be NOT warts). They could be molluscum contagiosum, brutus, folliculistis, and other stuffs. You have to ask a doctor to find out.
If you have and your doctor diagnosed them as genital warts, forget my above paragraph ^^
Now regarding your question, aldara should be able to get rid of the warts within 1 week. Your hypopigmentation should be better with time, like let's say 1 year. If they leave permanent scars, you shouldnt worry much either as when your penis get erected, they shouldn't be visible anymore (as your skin get stretched)
I have 5-6 genital wart scars that you can notice when im in normal state but when im erected they are barely noticeable unless you look at them closely.
thanks man. yeah i've been diagnosed. and i've been putting the aldara on about 3 times a week for about a month and a half... and the warts are a little smaller but definitely still there. it just sucks cuz i'll put barely any on but since the skin folds in that area it always gets on healthy skin... so i quit and will probably just get them burned off like in the past even though they are smaller than normal.
hopefully the color will return (but it does look better when erect)