Yes, the “complexities at the boundaries” are a real problem — I tend to call it the “glue” problem. I’m starting to think there will never be a boilerplate to rule all boilerplates, rather, as the ecosystem of actual libraries grows, more “glue” libraries will appear, that will glue together (i.e. abstract away) a piece (but never all) of the stack. The final step of gluing together the pieces you specifically need for your app will still be your task.
I would probably have settled for create-react-app a while ago if it supported server-rendering, but that would probably have been a mistake. After playing a bit with next.js I have to say it feels quite bleeding-edgy. But what it does better than create-react-app, is to abstract away one specific part of the stack (client vs. server-rendering).