I agree, if you wanted to start from scratch with your own structure create-react-pwa is probably a better repository for you. However, if you like the opinions formed in this repo then it will allow you to get started straight away with static type checking, e2e testing, unit testing, tree shaking, and code splitting all built in.
You raise a good point regarding Preact, it is something that I have considered but decided to stick with React until it became problematic.