I would like to know whats the best / recommended practice in this case...
I'm a former consultant, so the answer is "it depends". It depends on how many applications you have and what you are using the verified attribute for.
There is no way to register the user and the registration in one step unless you send the emails outside of FusionAuth. You can of course update the user via the API to have verified true when someone verifies their registration, perhaps by listening to a webhook: https://fusionauth.io/docs/v1/tech/events-webhooks/events#user-registration-verified and with skipVerification set to true.
I also wonder why you need to have both the user object and the register object set the value of verified to true. Can you have your application read just one of those values? Or are you looking to have things consistent between the two objects?