Just a few comments: As long as you can stradle the bike with your cycling shoes on, I wouldn't worry about the standover height. Ideally, you want a couple of centimeters, but I don't currently have that kind of clearance on my Bianchi, and it's never been an issue.

I won't comment on the pros and cons of 650c wheels, but I would agree with the others that, with your measurements, you should be able to find a standard geometry bike with 700c wheels. Also, toe overlap is a somewhat inflated issue. A minor amount of overlap isn't going to cause any problems. I have a bit right now on my Bianchi and I only notice it when I'm making a turn from a stopped position and that's easily fixed by making sure that my pedals are in the right position based on the direction of my turn. I'm currently working on designing a custom bike and have talked extensively to the builder and my fitter about the issue.

Based on your measurements, you might take a look at Bianchi by the way. I went through what you're going through a few years ago and have somewhat similar measurements as you. The 50cm Bianchi I ended up going with had the longest top tube/shortest standover (in a compact frame) that I could find. I have a longer torso relative to my short legs and Bianchi's geometry on their women-specific bikes is the only one that worked for me.