No it will not. I just successfully did the upgrade.
Follow the instructions. You simply skip the instructions that say to go to disk utility. Basically as soon as you are presented with installer for Yosemite press continue and it will perform an upgrade.
http://www.tonymacx86.com/374-unibeast-install-os-x-mavericks-any-supported-intel-based-pc.html
Important steps are to reset Bios to defaults (I thought it wouldn't be required since I had a working mavericks system but I couldn't boot from Flash drive). Remove all ram except for 1 stick. (I didn't do this initially and got errors when trying to boot.
I also ran into a problem with reboot after running multibeast. On reboot it would freeze on apple load screen. I reinstalled Yosemite update and ran multibeast again(slightly different options) and it rebooted fine.
Daniel