Usually when we hide entity collection via user profile configuration only the left panel entities (under home) get hide. Red Rectangular box is showing all those entities where your particular user is mapped or having visibility permissions.
If you want to hide all these Red box entities you need to remove visibility permission of your particular user from these entities via administrator rights. If we talk about system objects you can see upper left corner of Red rectangular box it says "Exclude system object" so this box does not have any system object.
