Each application should have their own spearation .dep list. If there is nested dependencies then it will take several iterations. What you see as undeleted may still 'depend' upon can be seen by the supplied reports.
Still there is much clean up that needs to be addressed with the .dep lists.I often see such reporting in the forums and therefore appsaudit is only as good as the dep lists.
Having an open community development providing such lists needs to be taken into consideration. Perhaps after moving to a single extension type, will make many things easier to manage.
All this need to be taken into consideration. Appsaudit is no panacea, nor will it ever likely be. However the reporting is useful and as the .dep lists become more reliable and not nested, things will only improve.