Anything wrong cooked is a major issue, not just JS. But good luck untangling a wrong cooked CSS file with thousands of lines, deeply nested selectors and multiple !important flags for the same properties without CSS providing even a single warning message. If you hit the limit of CSS there is nothing you can do, but if JS performs poorly, you always have options.

There is also a misconception that CSS is fully offloaded to the GPU which isn't true at all. Repaints due to content changes, layout properties, text rendering and many other tasks are handled by the CPU. On the other hand, manipulating opacity or transform properties through JS is offloaded to the GPU just the same. WebGL in JS is also pretty much handled by the GPU and I don't think CSS can interact with it in any meaningful way.