Hi Brian, the word work item category is confusing me so I am not sure if I understand your question totally...
It is true that some built-in attributes appears in both the workitem types but if you create your own custom attributes they should only appear on the workitem type on which you created them.
For an example, on the eclipse client, under Types and attributes section, if I select Defect and create an attribute there and then if I move on to Task I can't see the attribute I created for Defect. The presentations for the respective workitem types also follow the same behavior. Did I answered your question ?

I assume you are referring to the Scrum Process Template?
In 4.0.3, each of the default work item types in the Scrum Process Template have their own category.   In particular, the category of the Task work item type is com.ibm.team.workitem.workItemType.task while the category of the Defect work item type is com.ibm.team.workitem.workItemType.
In general, if two work item types have the same category, then as you observe, any change to that category (e.g. adding a new attribute) applies to all the work item types which share that category.
To break that sharing, I believe you will need to create a new work item type, give it its own category, and then you can modify the two work item types independently.   Unfortunately, that does require you to define all the editors and such for the new work item type, but a lot of the work item type properties can be "duplicated" from an existing property, so that hopefully will speed up the process a bit.   If you are feeling adventurous, you could try editing the Process Configuration Source xml directly (you can always revert back to the original xml if things go awry).