I’m having a similar issue – when FVM is active for both CSS and JS, neither are being minified or merged. See https://va.onair.cc for example.
I would also like to be able to clear the FVM cache from the backend as I used to be able to do. I would prefer to not be required to show the FVM interface on the front-end which currently is the only way to clear the cache (without saving and using the clear cache URL).