Maybe I’m misunderstanding your use case, but to me folders would make sense. You can have a folder, say called “All Users”, that everyone would be a member of. When you create a dashboard or favorite you want to publish to all users, just publish it to that folder rather than checking all users. You can also control who can and cannot share to a folder. (Just because someone belongs to a folder, they don’t have to have share rights to the folder.) So in your example you gave, if a user copies a dashboard or favorite to customize it, it won’t automatically be shared back out to everyone, if they don’t have the permissions. They could only use it for their personal use. (Or they can have the option to share it with some individuals.)
As far as the additional maintenance issue goes, I would think folders would make this easier. In our case, we have folders setup for different departments. For instance, we have a “Credit” folder. We shared all relevant dashboards for our Credit / Collections department with this folder. So, if we have a change in personal, say we hire a new credit officer, when this user is setup in Phocas, we simply add him to that one folder, and he gets all applicable dashboards. Otherwise, I’m going to have to locate and add each individual dashboard to this user. (Obviously this can be easier by coping an existing user, but this also applies for the folder as well.) If I create a new dashboard for credit, I share it to all of them with one click, rather then having to select each individual user.
To me, using the folders is much less maintenance then not using them. But maybe I’m missing something in your scenario.