The way I think about it is that benchmarks include deterministic operations (that happen every time) and nondeterministic operations (that don't). And all of these numbers are positive, since there are few things in the world that take negative time.

By taking the minimum, we focus attention on the deterministic operations. This isn't likely to be realistic for production, but production won't look much like your benchmark hardware anyway.

When making code changes, deterministic operations are the part you have most influence over and have the most impact. Removing an unnecessary, deterministic operation will speed up every run, not just some of them.