What you -are- benchmarking is namespaces, cgroups, CoW filesystems and your underlying hardware.
As Solomon has already pointed out as soon as you use a bind mounted volume in Docker parlance you are simply benchmarking your host Linux kernel + host filesystem + host hardware, nothing more. I am unsure of whether Docker is now configuring the cgroups cfq or blkio controllers yet but that could also play a part.
The TLDR is this: Docker doesn't have an impact on performance because it's just glue code, none of Docker itself sits in any of the hot paths. You are better off benchmarking the individual components in the actual hot path. Also worth nothing that compute benchmarks will be absolutely worthless as they -will- be 1:1 native performance (because there are actually no additional moving parts).