The only trouble is they don’t actively talk to each other. Each app doesn’t know if the other one has turned lights on/off. Hopefully they’ll add the twinned sensor that hue labs have as well.
Yes, it's a little frustrating but I expect this to improve markedly over the coming months.
One *advantage* of a HomeKit hub (Apple TV, iPad or HomePod) controlling all the automations is that it frees up space on the Philips Hue Bridge. It has a limited capacity for animations, automatons, scenes, etc. whereas HomeKit doesn't seem to have any limitations here... at least not that I've found yet.
Another advantage is that you can mix different manufacturers together when it would normally either not be possible, or only possible with an external link site such as IFTTT.
For example, I have set a Philips Hue Tap switch button to turn on my coffee machine which is plugged into an Elgato Eve Energy plug. While the Home app is relatively simple, it is manufacturer agnostic, which makes it a seamless experience. I LIKE the fact that it's all controllable within the one place - kinda like Apple Pay. I'm not interested in the banks making their own payment/wallet apps... I want ONE place for ALL of my cards, regardless of bank.