Are Immobilizer chips part of the oem security system??

My cousin posted on here previously, as she had a "check engine" light on. Everyone on the vortex suggested to check the gas cap, then when that didn't work, to take it to the dealership to get the Oxygen (O2) sensor covered under warranty.
Apparently, the O2 sensor was the problem, but she was still charged $140.00 for 2 hours of diagnostics??!
The reason, the computer check (?) would not clear past 52%..and when they talked with the VW rep on the phone, they said it was b/c of an aftermarket chip or the EFM (???). The culprit, a black disabler circuit chip (immobilizer) that resides right underneathe the steering wheel by where your right knee would typically sit when driving. We were told this was a non-factory item, and the source of the computer code not clearing.
Is this "immobilizer chip" factory? She bought her car in California from a vw dealership, and the only reason she was charged was because the immobilizer was not factory.
Can anyone help us with this problem...did we get taken or is there any way we can get a refund?? I mean, the O2 sensor was the culprit, and the computer (technicians computer) didn't clear...that wasn't something we were responsible for, right?!
Thanks vortexers!
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