This would be nice (I also haven't found a way to do what you'd like). More than once I've accidentally opened up a new instance of a pinned app because of this. It's a super minor annoyance, but still something I'd like to be able to change.
There is a checkbox with a very confusing name in the task manager applet's settings that does just that. I can't remember its name just now (~~something about separated launchers~~. ~~It's "Combine into single button"~~. Nope, it's "Keep launchers separate" and it's indeed needs restart).
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