Do you know how to UNLOCK or have the instrument clusters already been UNLOCKED on these vehicles? I ask because in a situation as you described above...you can run
TEST 9 (ignition in position 1 & engine NOT running) and get a quick look at the battery's voltage. If the battery is at 11.89v...its at 0% state of charge. This is many times enough "juice" to illuminate interior lights & dash lights & radio & starter, etc...but may not be enough to start the engine.
Again, thinking that I may have missed something...I'm really curious as to what your dealership is "initializing" because again, there's no IBS or power management system on the e53...perhaps they are just charging the battery making sure that its voltage is up to about 12.65volts. ...but apparently as you describe...they're doing something.