Benchmarks are vital. They can give you an estimate of how your application performs. They also often showcase how optimized a product is on different platforms.
But that's kind of obvious, so why are you asking this?
They consider difference due to compiler versions to be "wrong", differences in flags to be "wrong" etc. . So "the difference comes from the parts that hadn't changed", yeah which ones would you permit to change to consider the benchmark not "wrong"?
The problem with Phoronix v the build flags is not that they are different between systems/distros; quite the opposite: Phoronix builds the software in an unsupported way, ignoring system/distribution defaults. Which means, they measure software that’s miscompiled/misconfigured.