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I've just tested this as vampire counts, confederating von Carstein. If you confederate a faction while it's legendary lords are wounded (in this case, both Vlad and Isabella, just to confirm whether or not lords flagged as faction leaders may function differently) you will still not have them added to your roster.
This was fixed almost a year ago for WH1, and not having it drastically limits the possible scenarios in which you can acquire your faction's other lords.