You are correct, the transfer hasn't happened yet and is pending. I have been clearly instructed by both a lawyer and the ATF to add it to the Schedule A and denoted as pending. The schedule A can be either a blank copy with just the pending item or a copy of all the items with stamps and then added as pending to the bottom of it. When it's back you can either add it to the original schedule A or line out the pending and add the number. Either is legal. Ultimately, I don't think it matters at all if you add it or not, but after talking to the NFA office about it, I do what they told me to do.
Man, it's so funny. Half the time I don't think what the dealer and buyer are getting wrapped up about are not relevant at all to the NFA office. As long as the form 4 is tight, the check cashes, and the gun trust is done well the transfer goes through just fine.
BTW, did you know you are supposed to bring a letter certifying that whomever is picking up the NFA item is allowed to do so and associated to the trust? If the trustee is picking up the item, they certify that they are OK to pick up the item. Ya, I know stupid right? I have the reference showing this requirement at work. I about fell out when I found out about it.