Some times a messenger pop up comes up on application which is completely random. It may appear in any page and also not as soon as you land on a page. It may take a while to pop up. It is basically company updates or any new feature release related. Is there a way to handle it using Capabilities class or how to handle it?
It is not random. As you said: "It is basically company updates or any new feature release related"
Feature flags solve your problem, by allowing you to select parts of the of the application to be included or not in a build, through configuration files, e.g.
Thus, you only need to configure these updates to be display only on the environments they make sense.