Why does my new Macbook Pro ship with Mavericks instead of Yosemite?
Unless it was a BTO (Built-To-Order), it's likely coming out of a warehouse or shipping container that was packed pre-Yosemite and those boxes aren't opened to update the OS.

Yosemite is a free upgrade, so just upgrade the OS when you first power up the machine and there won't be any difference between your system and one that left the factory with Yosemite.

There should be no "performance lag" due to an upgrade vs. clean install, especially for a fresh-out-of-the-box system but if you're worried, this site has all sorts of questions and answers on how to erase and then install Yosemite.