My idea is that an app should do its best to work with the OS and not override defaults, that includes system fonts. It is good for consistency, accessibility, etc... If Windows doesn't ship with flag emoji, or any character for that matter, that shouldn't be Chrome's problem.
Android is an OS, Google is responsible of it, so they get to decide what goes in their fonts.
By that argument, they shouldn't override the OS trust store either, but most browsers do. There's a compromise between consistency and user friendliness.
Android is an OS, Google is responsible of it, so they get to decide what goes in their fonts.