On opening the app I'm told that "WhatsApp works with Google Chrome 49+" and I should update Google Chrome.
OS: 4.19.59-1-MANJARO.
nativefier web.whatsapp.com
Then open the app
Relevant screenshot:

Fixed: Change the user agent to Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/74.0.3729.169 Safari/537.36.
Something else that I've found works is changing the user-agent when packaging.
nativefier web.whatsapp.com --user-agent "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/74.0.3729.169 Safari/537.36"
This seems like a long-term fix (until WhatsApp requires a new version of chrome).