They are separate subscriptions, one is hosted by the original provider in their native app vs Apple who has partnered with the provider to host it within their app (using their servers) and allow users to subscribe there for a more seamless experience.
If there is a glitch that is currently allowing that scenario that may be a temporary workaround but won’t necessarily guarantee a long term solution.
Amazon also offers channels and they work exactly the same.
It’s not a matter of paying twice, but rather making a decision based on which app you want to use and subscribing accordingly.