Okay, I will preface my next statement by saying my memories of this are fading and I'm not 100% sure (can someone else who remembers confirm or deny?) but.....I think the APHIS (or equivalent "fit to fly" certificate/letter) does not need to be endorsed by the USDA office.
But I REALLY cannot remember about this, so don't quote me on that until someone else maybe comes along to confirm? /?

??
It is usually something you get done on the same visit as the tick and tapeworm 24 to 48 hours before your check in time; if I recall correctly.
If I'm not wrong, the only things the USDA office need to see are your 998, your form "FAVN" rabies titre result, and your rabies certificate to verify the other's information against -- at least, these three were what my specialist told me to take to my USDA office.
You must get the USDA endorsement within four months of your pet's flight date.
The final section on the 998 deals with the tick and tapeworm and this obviously doesn't need to be filled out yet when the USDA stamp the form, as it's the last thing to happen. As I've said, I believe the fitness to fly document, whether you have an APHIS or a letter, is another "last thing" item as I believe it is supposed to confirm health of the animal within a two week window of travel date.
I am fuzzy on this particular detail, so corrections are welcome.