Yes, the XS Charge PMA system would be a great upgrade to the stock charging system.
This rotor replaces your old rotor that has failed or magnet that has weakened over time.
It also replaces the regulator/rectifier with solid-state electronics.
https://www.mikesxs.net/yamaha-xs650-xscharge-permanent-magnet-alternator-kit-pma-200-watt.html
Yes, it is fully compatible with both electronic ignitions and stock points ignition.