Everything is 3D Slicer are linked via the MRML scene containin the MRML nodes. In addition to the data nodes, there are display nodes driving visualization. What @muratmaga meant is that for volumes, 2D (slice) and 3D (vol. rendering) are different mechanisms. They have different display node types etc. So if you show a volume in slice views, it won’t show up in 3D and vice versa.
Color is managed differently for the same reason: the two visualization methods are very different. 2D slice visualization uses lookup tables, while volume rendering uses transfer functions. You can synchronize the two in the Volume rendering module by clicking the button “Synchronize with Volumes module” on the top of the Volume properties tab in the Advanced section.
The combobox in the volume rendering module selects which volume node the module panel will handle. So if you select one and turn on visualization for that, and select another, then the eye icon will reflect the visibility state of the new volume, so if you want to switch between visualizing two volumes in 3D, then you need to hide the first and show the second. This behavir may be confusing, and has historic reasons (we could only show one volume in the past but now there is an experimental multi-volume option, for which the UI has not been fully adapted). See discussion here