Roots grow towards water supplies, so it is likely you had a leak from the toilet, otherwise, they probably wouldn't have grown there. Make sure you get a good seal when installing the toilet. If the tile will raise the floor level, you might want to tear the existing flange out of there, get a good look at what's going on, then install a new flange on top of the new floor. You might be able to put some root killer down around the pipe, depending on how much room there is. Interesting problem...will see what the others have to say.