Former AASP for Micro Center here, I can confirm this is exactly how it works as an Apple Tech. Apple's system for repair is super difficult to work with, and they do require you complete certain course work before ordering parts for newer computers. It also doesn't help that this system is incredibly hard to navigate (as of last time I worked with it 2 years ago) and it's not guaranteed that the system with the training's will talk to the system with that allows you to order parts.
My guess is in line with Diglio's, there's most likely some issue systems, training, or otherwise than the part not being physically available. The other thing is that the Apple Store most likely doesn't have a designated "Parts Coordinator" If the repair shop is big enough, they'll have a full time person in that position, those people are usually the best at getting you through stupid stuff like this. My suggestion, just find larger chain retailer that's Apple Certified and has a sizable repair shop. They usually have those resources.
p.s. My favorite part with IMac screens,was when they're shattered like Ltt's is, you're instructed to cover the entire surface in painters tape to prevent it from completely disintegrating.