Hopefully when he's older they might consider a lens implant for him. I was aphakic (no natural lens in both eyes) from 2 through to my late 20s so know exactly how/what he's seeing (in a general way). Wills is an awesome hospital- I've been there (and Scheie's, also in Philadelphia).
The finger flapping I wonder if that too is a behavior to see light patterns. I was once told that I did something like that as an infant/toddler before all the surgeries and glasses (and yup...20/200 without glasses lol- big E was all I could see).