We have the same issue in a different context. Basically what you and I are looking for are what I call Link Attributes. Attributes which are not tied to the item master definition but instead linked to the specific instance, or use, of a part from the item master. Many far more expensive PLM/PDM tools manage these types of attributes wonderfully.
All that said, unfortunately there is only 1 attribute with this characteristic: Component Reference as you have mentioned above. We have devised a trick that does work. It requires a few user helpers to manage but it does work!
We treat that one attribute Component Reference as an XML information passer. Any one attribute could have any number of the following:
<replace qty>REF</replace qty><Ref Des>12345</Ref Des><Blah Code>A1</Blah Code>
Again, you will need a Solidworks API to give users a friendly GUI to manage this data. On the other end, you will need an EBOM builder to decompose the information into tabular attributes.
It takes some development to make it work but once set up you get all the link attributes your heart desires!
Hope this helps,