you get a better fitting when you remove the comode and tile under the toilet. Its much easier than cutting each tile to fit the curvature of the water closet.
here is a potential problem, If you build up the tile or floor too much you will not have a good connection between the comode and the sewer colar in the floor. If so, you have to add an extension for a proper fit.
Then add a new wax ring and carefully tighten down the bolts and then caulk around the comode's base and you have it.
you can also, draw a template of the bottom of the comodes base and then cut that out and transcribe that template to the tile and cut out on the dotted line.
I am assuming you are speaking of vinyl tile in this case. If you are talking about ceramic then you will definately need to add the toilet extension and I would definately tile up under the toilet and then sit it back down.
Steve ps use a good silicon sealer on the grout if ceramic tile.