Also WhatsApp is closed-source, so you can only take their word for whether the E2E is really E2E -- and it's owned by Facebook.
DNS can be filtered to provide some degree of control and traffic inspection, but there’s always DNS over HTTPS, tunneling, and so on and so forth.
I’d be surprised if Signal was doing it, since getting caught at it would totally destroy their reputation, but I’d honestly be surprised if WhatsApp didn’t have at least a backdoor for it.
https://signal.org/blog/reproducible-android/
Unless you espcially meant by ”App Store”, by Apples App store, it is Apple to blame in that case because it is not possible due to the encryption of app binaries.