WhatsApp works properly on GrapheneOS including end-to-end encryption. I don't recommend using it but you are better off running it on GrapheneOS than AOSP or the stock OS. Signal has comparable functionality / usability with better privacy / security and there are other options.
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I don't know what you're talking about. GrapheneOS supports all the same baseline security features of the stock OS including all the hardware-based security features and it provides full security updates just like the stock OS. Where do you get the idea that it doesn't do that?
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The entire point of GrapheneOS is starting from that baseline and building privacy and security enhancements on top of it. It would be entirely pointless if it didn't provide full security updates or didn't preserve baseline security features including things like verified boot.