The fare discrepancy can extend beyond longer/shorter route calculation -- there is also the issue of surge price disparity between driver and passenger. For example, the user would see 3x surge pricing while the driver would see 2x surge pricing, where the user is charged for 3x but the driver is paid for 2x. This is pure speculation and I have not witnessed this behavior but it's another way things can go wrong in Uber's favor.
Uber might be able to defend itself saying that the data provided to the driver and passenger are different because of misconfigured caching and stale data being served to either party, but it's a moot point in case Ars Technica has concrete and verifible claims of methodical and programmatic fraud. Personally I have witnessed being billed for $0 in-app after taking a round trip (effectively zero distance traveled) but the email notification showed the proper billing value, and there may be more instances of this "confusion."
Uber might be able to defend itself saying that the data provided to the driver and passenger are different because of misconfigured caching and stale data being served to either party, but it's a moot point in case Ars Technica has concrete and verifible claims of methodical and programmatic fraud. Personally I have witnessed being billed for $0 in-app after taking a round trip (effectively zero distance traveled) but the email notification showed the proper billing value, and there may be more instances of this "confusion."