It's still not obvious how they could be separated at all by pre-biotic processes. You need to go from (in principle anyway) a pretty well-mixed 50-50 mixture to basically only lefties. I believe this is still one of the bigger problems for abiogenesis, and frankly I think you're being too glib about the antimatter problem too. I expect we're eventually going to find out about specific mechanisms that cause those.

A very plausible explanation is that the separation was biotic