You're right, I was blurring clean install and new partition, because both go above and beyond what Apple recommends, which is to simply download it and install over whatever is already there. So, my point is still a valid one, if more than just installing it is the better way to go, then Apple should say so, or, they should only release a new OS when just installing it over what's there will be safe...
If I did partition my hard drive, and installed Yosemite, would that mean it would have no access to everything I already have, on the other partition? Would I be able to access those files? If they aren't accessible to Yosemite, how will I know if it works? If it works with nothing of mine in place, that doesn't really tell me much, as I'm sure it must at least work ok without anything else in play.