I'm not sure if this is already a known problem but I could not find a related issue.
gatsby new my-default-project https://github.com/gatsbyjs/gatsby-starter-default#v2
cd my-default-project && npm run develop
open Browser and look into dev-tools
When navigating to a different page, only parts of the DOM should update.
Every DOM node gets recreated. Including the root element.

System:
OS: macOS High Sierra 10.13.6
CPU: x64 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
Shell: 5.3 - /bin/zsh
Binaries:
Node: 8.9.4 - ~/.nvm/versions/node/v8.9.4/bin/node
Yarn: 1.6.0 - /usr/local/bin/yarn
npm: 6.1.0 - ~/.nvm/versions/node/v8.9.4/bin/npm
Browsers:
Chrome: 67.0.3396.99
Safari: 11.1.2
npmPackages:
gatsby: next => 2.0.0-beta.40
gatsby-plugin-react-helmet: next => 3.0.0-beta.3
npmGlobalPackages:
gatsby-cli: 2.0.0-beta.6
Here you go:
https://github.com/gatsbyjs/gatsby/issues/6127
Most helpful comment
Here you go:
https://github.com/gatsbyjs/gatsby/issues/6127