If keeping the family aspect is an important goal, why not stay on a smaller scale? Why feel the need to go to 100+ per batch? With your metaphor of being Mom, can you know the names of 2000+ children?
Because the benefits of more founders presumably outweigh the loss of intimacy. I also think she mentioned "do things that don't scale" in the article (if she didn't someone did in the comments) - if you build an incubator where you treat 20 founders like family, when you get to 1000 founders you will still be trying to do that.