Hey Gijo, that's a good question about media queries - for now it does not detect the size of the viewport of the client and it doesn't process the media queries based on that. But maybe that would be a good idea - to identify the client and return only the media queries that apply.
The css classes by JavaScript: classes that are added after pageload are left in the stylesheet, but if you have HTML partials returned by AJAX requests that introduce new CSS classes to the DOM, you should mark those in your stylesheet with a comment and then the service will leave them in the stylesheet.
Typically there wouldn't be too many CSS selectors that are returned after pageload, so it shouldn't be a performance issue.
The API is not perfect, still in beta here, but working on it. It currently uses Headless Chrome and UnCSS.