They said the retrofit of Discover Pro into a CMS-equipped car isn't easy owing to the car's computer system, something to do with it wiping itself everytime it's plugged in for diagnostics.
Reason it wasn't picked up on the PDI is that the order system used to check the car matches the order looks at the factory order placed, not the order in their CRM, meaning the PDI guys see it as being correct because of where the mistake was made. Frustrating but it's clear they're not covering up, just a genuine mistake in a very critical part of the order process!