The subset editor has the option "show duplicates" which is checked by default. When unchecked, double elements (e.g. in parallel hierarchies) are hidden.
There should be an extra checkbox underneath it, "Show duplicate attributes". By default, this should be grayed out. Only if an Alias is selected, this checkbox is enabled; when checked, duplicate attribute values are to be excluded from the subset. Example: include only one (first?) Product which - for the attribute "color" - has the value "black".
#3340
