In the auditors defense, I'm sure he/she picked that up due to the fact that we are told all the time (as auditors) that if a Plan is self trusteed they (the custodian) cannot provide a certification.
As the previous respondent indicated that is categorically untrue. I'm not certain why the auditor cares either, if they do in fact have a certified statement from a custodian...
If your in the New Engalnd area, respond - I'd be happy to have my firm do the limited scope audit...