I think this is much adoo about nothing.  The officer SS# does not get printed with any return copy.  It would not be available for public record unless you print the 990 information sheet with the copy provided for public.  I don't think anybody gives that sheet with any return copy.  That is the only place entered and is not available to public.

As far as transmitted, I think maybe the IRS does verify the signer and SS# to make sure they are legit.  But that is merely between you, the software and the IRS.  If we cannot trust the info with the IRS, then we are all in the wrong business.