> I tried bootstrapping it with `create-react-app` and ejecting, so I can modify webpack config

I am pretty much confident that everything worked well before you have made any modifications in the webpack config. So, the negative effects, that you are describing after, is a result of your efforts, but not anybody else.

And why did you want to eject in the first time? Most popular use-cases are already covered into create-react-app by default.