Both the Philips Hue and Lutron Caseta systems have certified HomeKit capability, while still allowing their own respective applications to work, as well as allowing other systems to be integrated directly with Hue and Caseta. Philips does restrict HomeKit integration only to their own Hue branded devices, though.
This will somewhat change with Matter, as Hue has stated that non-Hue devices, paired to the Hue bridge, will be exposed as Matter devices. Apple's Home Matter controller will allow these devices to be joined to their system.
So, things are changing, hopefully for the better eventually.