Our local code technically requires that the flange be set on top of the finished floor.
What I find odd these days is that a lot of the lower end toilets do not have the space below them to leave enough wax between the base of the bowl and the flange if the flange was on top of the finished floor. So what happens when you set the toilet is that you squish all of the wax out from underneath, and the toilet is only sitting on the flange. The base is 1/4" off the floor. Then you end up having to pull it back up and re wax it, and use wedges. . . i hate it.
In your case, being that you're using linoleum tiles, it won't make a difference. Keep in mind you might need some wedges.
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