In fact, I wanted to share a wiki or even a complete build of the custom app setup that I used once as well.
Agree the repos are read only… but curious why one would need to worry about that - because any other app specific changes should be negligible in Yii Basic App, except maybe the config folders
So if you fork for example yii2-app-basic and create your own for composer install. Composer will anyway handle updates to the vendor folders. You can manage any other changes to the other parts of this repo yourself.
Personally I installed a fresh Yii app and did the changes there and kept a Yii app template for reuse. Not sure if this helps.
You can create your own repo with a git subtree merge of the yii2 development repo and work on that. theoretically the read-only subtrees of yii2-app-* repos could be merged back into the main repo when we want to have the changes but as the current split strategy is optimized for speed and not for functionality there is no waranty that it will work.
As far as I see git subtree is the only suiteable solution right now.