Yes untreated warts usually clear within 24 months but there can be issues with size such as difficulty with urination and sex.
It is best to treat when warts are small because this usually means less treatment is needed.
You can work to boost your immune system to help your body fight the strain (s) in hopes they will become dormant sooner.
Vinegar tests for warts can't be trusted. I have warts, vinegar never turned them white. I used apple cider and white vinegar. I also have cell changes and the doc used vinegar during the biopsy and it did turn those white but only he saw that.
You can have wart in the same or other areas, you can have them appear the same or be different. Only a doc can tell you if they are warts.
I don't know about natural options but I can tell you that they would be slower to work medical treatments. Acid was great for me, Aldara is slower.
Your first question: your warts probably won't go away on their own. In most cases, if left untreated, they can grow larger and become bothersome. If treated, it can take up to 2 years for your body to rid itself of the virus itself, not just the wart. Your second question; warts can flare up at anytime, and if different places due to stress, hormonones, unhealthy lifestye, if you still have the virus. Thirdly, if your doctor suspects warts, they will automatically treat them. I have read more negative info about self-treatment than positive. Your best bet, is to go get checked out. If the doctor suspects warts, there are a few ways he/she can go about treatment. I have had tricloric acid done on mine, and this may take a few repeated sessions, but it really helps. Good luck to you :)