Cause

This is largely a result of ramping up the security UI for PWA windows so that permission icons (like geolocation) and the site's origin can be shown to the user in a non-spoofable way. Essentially the title bar has taken up the security UI role of the location bar and app menu.

Since Chrome/Chromium 70, Progressive Web Apps (PWA) use Client Side Decorations (CSD) for their window borders. This clashes with the window border defined by your window manager (xfwm in my case) because it gets the colors from the GTK theme instead of the WM theme.

Answer

To solve the problem Chrome has to:

Finding a cross platform solution for satisfying our security UI requirements without a title bar

But at the moment this won't be fixed.

Yeah, it might be reasonable to have some separate configuration to customize the look of these apps once installed. However, this is currently outside of our means (we do not have a lot of resources to dedicate to Linux, and other platforms are much more in the camp of giving developers full control over the look and feel of their windows).

Workaround

Manually create your own shortcuts to launch PWA in a separated window that uses your window manager border, i.e:

chromium-browser --app=https://web.whatsapp.com

Source: Comments #11, #14 and #32 - Chromium bug tracker