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.
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
Manually create your own shortcuts to launch PWA in a separated window that uses your window manager border, i.e:
Source: Comments #11, #14 and #32 - Chromium bug tracker