The issues are more being worse than flatpak in most ways: Proprietary, bigger, slower, no support for external repos
It’s more about WhatsApp ignoring Linux as a app platform (and the web app doesn’t have calls or screen share like the windows client)
I don’t like WhatsApp, but some people simply refuse to use anything else (“better”) and the web clients can bridge the gap but it’s extremely annoying not being able to answer a call with a person you are texting
The issues are more being worse than flatpak in most ways: Proprietary, bigger, slower, no support for external repos