I didn't see it mentioned in this thread, but if you buy used key fobs from eBay or elsewhere, and program with IID... they will only work if the battery inside the fob is good. If the fob battery dies, you can use the steel key to open the door, but the backup method of holding the fob against the underside of the steering column WILL NOT WORK to start the engine (see screen shot below). You need to install good batteries into the used/eBay fob. This means the original fobs are somehow hard-coded to the computer (I assume BCM, but don't know for sure) and IID can't fix this.
What the OP describes is different than just creating extra spare keys via IID programming. It may be that a new, ****** BCM needs to "marry" itself to 2 keys, which is why the dealer was asking for them. If this is the case, it's
possible that even used eBay fobs might work? I'm also assuming this may be a 1-time only process and once the wedding ceremony is performed, you can't have the BCM marry different fobs.
The wrench in the works is that you can buy new pre-programmed fobs from the dealer, and if the new BCM will allow a used fob to work, I don't know if future new dealer fobs would also work? Depends if the dealer computer phones home to the mothership to update key codes somehow...