JSLink can only be registered on certain list templates. This works well as long as only one web part on a page will be shown. If you added multiple list views of the same list template the template override will affect all web parts and not only the one that has the JSLink File attached to. To avoid this behavior the template override needs to be able somehow to conditional format the output.
When you migrate SharePoint 2010 to SharePoint 2013 or to Office 365 some of the views that was created in the previous version might look the same.
The user will get a mixed user experience because document libraries, switch between the old view styles to views that are configured for client side rendering. Via scripts those views can be recreate, but they also can be upgraded in-place.