You are making the assumption that the library doesn't have the flaws I mentioned. It does (You can go read the source yourself
https://raw.githubusercontent.com/bestiejs/benchmark.js/2.1.... )
There's no portion of the code that does warmups. There's no portion of code that "blackholes" the results to keep the JIT from optimizing away the code under benchmark. There is a lot of code though... so that's... good?
You make the assumption that just because a lib is popular or widely used it is "correct" or "the best". When it comes to microbenchmarks, that's usually flawed. Very VERY few people actually get them right, benchmark.js is no exception.
That, of course, doesn't mean that benchmark.js can't be useful. For macrobenchmarks it will be roughly right. However, for something as small as leftpad, it's almost certainly not the right way to measure performance.