The difference between map flag and markers is that the flag is client-side, you can't put it on someone else's map, you have to link it to them in chat, and then they clicking the link copies the data to their own client. On the other hand, marks are visible to everyone and updated in real time so there's a lot more communication between client and server involved. You will notice that even when a new person joins the instance, they can see pre-existing markers which suggests that they are part of that instance's "save data", as it were, so when the instance ends, the marks are purged from server memory too.

But I think your suggestion is still viable if they allowed the client to save all mark coordinates in your current instance to clipboard. That way you could refresh the marks after leaving the instance by executing a macro.