If "counterfeit prevention" system is complaining about a genuine part that literally came off of another genuine product, that's not its actual job.
If "anti-theft" system is trying to wrestle with the legitimate owner trying to fix their own product, that's not anti-theft, or rather, the owner is not you. The owner is Apple, and that's precisely what the article says.
The "security" here is protecting Apple's bottom line by ensuring you buy a new product for otherwise fixable damages.
Just because it's somehow more secure doesn't mean it's better for the consumer in any way.