I have had the ANA measured 3 times... at 1:320, then 1:1280, and the last time was 1:2560. My only other positive antibody is also the ACL (anti-cardiolipin) which was only tested on two occasions several months apart. Yet with those results as well as my symptoms (joint pain, malar rash, sun sensitive rash, pleuritis, costochondritis, etc.!) I was diagnosed and treated. I'm glad that she has started treatment based on your symptoms and positive blood results, and she is probably right that the only reason to get the lip biopsy is if it's important to you to know for absolute certainty what you have since her treatment probably wouldn't change no matter what it came back as.
These antibody tests... seem to have no rhyme or reason sometimes. There is no reason to suspect that you would have had more positives if the additional testing was done with the other lot of bloods which showed the higher ANA even though I can see why you might think that.
I think what your doctor said did makes complete sense with the exception of advising you to not get pregnant on Plaquenil. The advice to not get pregnant just because you're on Plaquenil is a bit out-dated. If however, she really meant that you should wait until you are more stable in your disease activity then that's spot on too. Most all doctors will advise women to stay on Plaquenil while trying to conceive, during the pregnancy, and after even if breastfeeding. You may want to ask her about that again at your next appointment.