In the Seattle area, the closet flange is installed during framing.
When the roof is installed, and the home has been dried out, they come back and install 5/8" underlayment for the vinyl. Now the flange is lower than the finished flooring.
It takes two wax rings.
You can use one, and keep replacing the floor, and have that nice musty sewer smell from the lack of complete seal. Frankly, that's a poor installation.
I don't know how plumbers do it in other parts of the US, but all of the plumbers in Washington State do it my way. I've worked in companies with 150 other plumbers, and it was a no-brainer.
What I find strange, is how many people online that are posting that don't seem to know basic plumbing.
I couldn't operate a plumbing company if I did the work the way they brag about. My insurance claims would be through the roof.
Flanges that are above the finished flooring. Many of those that I see were installed before 1940.
If I'm in a home built before the war, then maybe I'm using a single wax ring, with no horn.
I see some "plumbers" all over the web, and I have never, ever seen pictures of their work.