I believe the design is like this - so that companies under one consolidated group with similar items/customers/suppliers/scripts (not employees/warehouses unfortunately) can share data …
I guess what you are trying to say is that there should be an option to isolate the masters from other users
Am I right?
Also would you know how to consolidate companies which are on seperate instances/sites/servers especially complicated ones where the Chart of Accounts are not similar?
Also check out What is the Best Practise to Manage Companies in Multiple Countries?
And Manufacturing Settings warehouse should be company-specific · Issue #46233 · frappe/erpnext · GitHub
where the user wants warehouses to be company specific - the opposite of what the OP wants 
Poor Frappe team - needs to statisfy everyone