Yes you need that tile floor to be nice and level underneath the toilet otherwise you will need to shim the toilet and then hope its not too noticeable after you caulk your toilet base to the floor. Remember tile always goes underneath the toilet meeting the flange or with a slight offset (seperation between the tile and the flange so that the closet bolts will slip in and out of the flange without getting trapped by the tile.) For a perfect illustration of this go to
http://www.plumbinglessons.com/sup/toilet.htm
Carpet on the other hand never should go under the toilet.
Something else to bear in mind is if the flange ends up below the tile you can usually make it up with another wax ring. If it is going to make it 3 wax rings high I would raise the flange. If on the other hand the closet flange is going to be above the tile you may need to lower the flange if your toilet base won't reach the floor because the porcelain will crack under that situation. Thanks for wanting to do the best job.