On the other hand, with immob-3 clusters, a lock-bit it set in the key's transponder, disallowing it to be written to again. This has nothing to do with a database, or anything mysterious like that. Whether you use vag-com, or the dealer uses their tools, the adapting of keys to clusters/ecus occurs identically. You can check measurement block 22 in vag-com to check whether or not the transponder in the active key is locked or not.
Note that this difference between immob-2 and 3 is due to the cluster, not the transponder. The very same writable transponder is used for both immob-2 and 3 cars. It's just that immob-2 cars either re-write the transponder without setting the lock, or simply never write anything to the transponder. Either way, the point is, you can probably re-cycle keys from immob-2 cars, but never from immob-3 cars.