That doesn't necessarily mean that one OS has a disadvantage or advantage over the other, but to the user it might seem like it. For example I might have to tell the Linux kernel that "aspm=force" through the bootloader, but on Windows someone else did it for you(the corresponding tweak) and called it, let's say, "Asus Smart Battery" and tell you it's a software developed by the company that helps make better usage of your hardware. xD
(I made up the last one randomly to clarify.)
But how would the user tell? Or care I guess .. :/
I believe that it will get much better soon though with some things things I'm reading and most things will be able to pretty much just work, even if no-one does it for you(or an OEM at least etc). Hopefully things will indeed go well in this part. Besides, more machines with Ubuntu pre-installed will be available in the next years it seems.