Just to ensure I'm understanding your situation, you want to compare the join of two tables with the same table join in another database, ignoring the column used in the join condition.
If that is correct, create a view in both locations that generates the results you want to compare. Perform the comparison using these views, set a logical Key value (e.g. XId?) and ignore the real PK column differences.
I just tried comparing views and they don't appear in SQL Data Compare, even though the tab indicates they are comparable. I've created another forum post for this.
http://www.red-gate.com/MessageBoard/vi ... hp?t=17810