I don't think you are quite getting what Mark is trying to explain. Think of it like this: there are two ways of changing a component to 'reference'; you can right-click, as Mark says, in the browser of an assembly in which the component appears, and select Reference under BOM Structure. This will have the effect of showing the component, in drawings of that assembly only, as a phantom line, and not including its mass in the assembly weight. This is the correct work-flow. The other thing that can be done is to change the components properties directly 'at its own level', by going to Document Settings in that component, and changing its BOM structure there. But any changes you make there will apply to that component wherever it is used. I think it is fair to say that 95% of cases, there is no need to tamper with the default BOM structure under Document Settings, probably 'Normal' for an assembly. You only have one 'version' of the component, but in some assemblies in which it appears, a different 'flag' can be set it, making it act as reference geometry in that assembly, think of it that way.
It is also important to understand that in Inventor, 'reference' and 'phantom', when describing BOM status, are two different and separate concepts, unlike other areas of CAD where the terms may appear interchangeable.