It is better to have a toilet flange on to of the finished floor. If the flooring only butts up to the flange then those edges are still exposed to moisture and can limit the life of the floor. I always replace the flange however this is not something a homeowner can always do. What size and type of piping you have makes a difference.
With the floating floors I have been fastening the flange through them into the floor without problems.
If you don't reinstall a new flange you can use flange extenders that are just the rings that fit on top of the existing flange. It's best to silicone all edges of the flooring if you do.
Wax is not really made to resist water pressure and double waxes will work initially but they often fail after a few years which you can tell by the damaged flooring. Some plumbers are using the fluidmaster insert lg has reccommended but they don't seem to work in all cases for different reasons. They do seal against water but they made not continue to seal against the sewer gases.
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