I'll give some examples.
In my profile "ProfileX" I create stereotypes "StereotypeY" and "StereotypeZ".
StereotypeY extends the abstract metaclass "Classifier". StereotypeZ extends the concrete metaclass "Class".
The profile helper will allow you to create a reference to StereotypeZ, which will then define the item "ProfileX::StereotypeZ(UML::Class)". If you manually defined a toolbox item for "ProfileX::StereotypeZ", EA assume you want a Class, use that icon and create it as necessary. However, you can also apply that stereotype to an Activity because Activity is a kind of Class. In order to add that to the toolbox though you would need to explicitly add "ProfileX::StereotypeZ(UML::Activity)".
In the case of StereotypeY, there's a whole set of possible metaclasses that you could want to apply the stereotype to. The profile helper does not have the functionality to show all the specializations of the metaclasses you are extending, and the only one that is being extended is not something that can be created. So, you need to explicitly specify in the toolbox which of the possible metaclasses that you want to create.
The metaclass allows you to specify which of the UML types you are basing your element on. As an example, you'll get very different behavior when you ask to create a Class and a Dependency.