Right or wrong the only way to be (half) sure that the font size you define is what the user sees is by defining a pixel font size for the body as the starting point. From then on you can define percentages as required.
There is a method that I posted in the thread mentioned above that shows how to do this even for IE6 and still allow the user to scale the text with the browser controls.
I find this method combined with the correct percentages to be the most reliable cross browser. (Too many of the other methods use percentages that will give say 13px in one browser and then 14px in another because of rounding errors or guessed percentages. Remember that simply saying xx% of a font-size is not going to give an exact measurement and if the measurement works out 12.9px then you get 12px in some browsers and 13px in others.)
However, a lot of people would argue that changing the base font size is taboo from the start and therefore it's a choice you have to make for yourself. I believe that setting a reasonable start size is a reasonable approach but many would argue otherwise.
Of course the user can set their browsers to ignore any fonts or sizes I define and indeed just use their own stylesheet so ultimately there is never any complete control over this and neither should there be.