The bicycle standover height is really important! If you can’t stand over the top tube without touching it, you run the risk of hurting yourself when you stop quickly.
If the top tube is higher than you are, i.e. you have “negative” clearance, you’re an accident waiting to happen. Landing hard on a piece of steel, aluminum or carbon fiber tubing isn’t going to be a pleasant experience. You won’t “get used to it.”
Even if you just graze the top tube when you stand over the bike, you may still run into problems. The road surface isn’t always smooth. If you stop and put your foot into a divot in the road, you’ll be that much lower and you’ll run into the top tube. I know, you can always “lean the bike over”, but if you’re stopping unexpectedly, will you always remember to do that?
It’s too bad so many manufacturers neglect the petite rider. After all, she’s serious about her sport too and deserves the same good equipment as everyone else. Occasionally, a customer comes to me who is still an inch or so shy of fitting my smallest stock design. Ah, the beauty of a custom bike. Since I build to order, tweaking the geometry to fit that rider isn’t a problem, nor does it cost any more. You can’t put a price on your health and safety, so if you’re in the petite fit boat, consider a custom bike.