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You are correct that applying a lot of account limitations tends to silo people up and hinders their ability to work across teams. Storage admin sends a link to windows admin and they can't check it out because they don't have permission to see that node.
Usually what I do is leave most accounts with the ability to see any node at all, but i leverage the custom properties the same way you describe to organize everything and then build dashboards with view limitations where if a windows admin just wants to see their nodes they know which page to go to. That way people can get focused in as much as they need while still not completely cutting them off from other systems.