Hi, I have done virtually that today :D.
I have a custom backend written in Rails.
So I had a case where a user needs to verify email to continue using the app after register. So on register, my backend sends you an email with a normal web link where you verify your email (link contains a confirmation_token parameter, which allows the backend to verify it).
However, I have set up my site to support apple’s universal links. So if the user presses that link in email on his iDevice, universal links will not even access the web page but will be directed directly into the iOS app. iOS app receives that url, and parses it (you have to write code to parse it), so it gets the confirmation_token from that url. And now we have some code to send to server to a special API point made for verifying email.
What you need is universal links + code in your app to respond to those links (that is an untrivial task though )