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Thanks for explaining it so elaborately. I see a few problems though, or maybe I'm just not understanding it properly.
In your first scenario, where you mention both addons including Notifications. I'd not recommend any addon to include it, but instead leave users to download it on their own, and have the addon check whether or not it is present (using Notifications as an optional dep, or a required dep if its functionality is its sole purpose). There should be only one version of the addon present at any time.
In a situation where two addons do include it, then the addon folders themselves will naturally conflict, and the user will only choose to keep one.
In the case there is only one version of Notifications, and there are several addons using it, one changing its settings - that is not a problem. It is made so that settings which can be changed don't affect important behaviour.
In your example where the latest version of Notifications is always used, there can still be a problem. If an addon is written for an older version of it, and some core functionality changed, then it will still break when the user updates Notifications.
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