That's not true. You can't use 0.0042% because then you don't have enough frames to be statistically significant without running for a very long time. It's also true that a frame pacing issue that is so rare that it isn't even impacting the 0.1% frame time isn't going to be noticeable, really.

These benchmarks are controlled for game bugs and architecture by simply averaging over ~40-50 games, on repeatable loops.