I see what you are trying to say here and while I can agree on some aspects, I personally see no harm in using CSS in JS. You know why we have CSS in JS? Because conventional CSS is a mess. The one global scope for all CSS is a pain in the butt. If you have ever worked on a large scale application, especially when teams from different timezones are working on the same application, you see first hand the issues that arise when someone checks in some CSS and it messes up your newly committed feature.
As for your comment regarding writing your app in components, the project I am working for now (for a small startup) is in components, the startup I worked at prior was an Angular/React app and once again, components. The last 3 freelance projects I did were written in a component based fashion. Components make sense in all sized applications. They promote encapsulation, they are easier to work with and reduce the amount of merge conflicts you will encounter when working in a team of more than 5 developers. A component workflow is not just for Facebook.