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Currently the permissions are global to the whole Thingworx platform. It's fine for most of the entities , but Project should be an exception I think.
The project is not a namespace, but it should be the boundary of the permissions, that would be a better balance between the isolation and sharing.
Please feel free to submit your request for feature changes to the ThingWorx Ideas board. This will allow others to vote for it.
If you are looking for a bulk visibility permission control, you might use Thing Group to do so: