For many years, I thought layers was the only way to group things... That happened because I was using AutoCAD and nothing else.
Now, I use Revit and MAX and I know new terms like "selection set" , "group", "named set" etc...
I discovered that layers were mainly for visibility control. For objects handling and to apply modifiers I believe that things like the others I mentioned are much better.
Using MoI, we need to be able to name the objects. We need to be able to make groups or sets that we can describe.