I'm not sure what you're talking about ? You're not sending your private key to their server without first encrypting it first locally. Their servers are not doing the E2EE, your client is. The website front and apps are open source.
Yes they could send you a compromised front if you use it via their website, that's a compromise you accept, otherwhise you could only use their apps which are open source.
In my opinion, those warnings are not used to help users but to shame developpers for not trully sandboxing and verifying their apps. Developpers know that having this warning will decrease the number of users downloading it. The goal in the long run is to improve app sandboxing and security.