I don't understand this. Could you be clearer about what you expect to be handled in what way?
In the case of users with an account, you tie their settings to their account so when they log in again their settings are used. For anonymous users... Well, they're anonymous for a reason. If they clear their cache (or their browser/OS has to) their config is gone, but they have their disk space. That's the tradeoff.
Cookies are only editable by the domain. No external system should be overwriting your origin's cookies. This is a part of the "Same Origin Policy" that browsers adhere to. If you include a package on your origin that is writing on top of your cookies, then you need to handle that conflict as the developer. It's pretty easy, just rename the cookie name you use.
Because, what you're asking for seems to be for browser to generate a unique identifier to a user at install-time that persists for that entire install. Which, opens an extreme privacy issue since there then would be a direct identifier to a given user that currently doesn't exist. There are side effects to be thought about where such an identifier has the ability to be extremely mis-used. They outweigh any developer benefit from having one.