I agree. I am saying he requested the Replacements because he knew they would be signed by SECNAV, thereby allowing him to show that his Medals came from the Secretary of the Navy.
I have been in the AF for 22 years, all my awards are one certificate, signed by (As you said) the awarding authority for that Award.
Everything to which I am entitled appears on my DD214. I can't imagine anyone questioning the validity of what appears on that form as long as the form is genuine.
The only reason I can see for someone to request a certificate for a medal which is already on the DD214 is to be able to frame it. There may be information available regarding why the medal was awarded. Perhaps that appears on some types of certificates.
Also, after 35 years, memories grow dim. Apart from official records, it can be very difficult to determine exact dates. As with Bush, people will be expecting Kerry to account for his time in a manner consistent with his claims for how the time was spent.
Kerry's request to amend the DD214 to include campaign devices for the VietNam Service Medal seems very strange. The dates speak for themselves and it apparently was not the practice to include the campaign information on the DD214. The dates of specific "campaigns" were probably not determined until after the fact. This would make it difficult to include on a DD214 which a serviceman receives on date of discharge.