As some of you may already know, when you disable the immo bytes in the eeprom on a B6 A4 the cluster screams "SAFE" at you and flashes the hazards without a paired key. The car will start, but the cluster doesn't like it. I guess that is pretty similar to a MKIV when you don't have matching keys on a immo defeated ecu, except its just the little tiny immo light that flashes on the cluster.
To get around this and do it properly, does the immobilizer have to be disabled from the flash itself? Any examples?
The key must match the cluster. Immo can be off, as long as the key matches the cluster. If it doesn't, you get SAFE. No other way around it. Immo off in flash won't help.