I removed the carpeting and installed some vinyl plank flooring lifeproof from home depot.
Install vinyl plank around or under toilet.
If you are installing vinyl planks in a bathroom you may need to temporarily remove the toilet or you can install around it.
Install the vinyl plank flooring.
Install full vinyl tiles on the bathroom floor stopping when the full tiles will not fit next to the toilet flange.
Underlayment installed with toilet drain cutout.
The hole for the toilet drain and notches for for valves and piping were cut with a saber saw.
Installing under a toilet after you remove the toilet which is often a two person job you need to measure the position of the flange and cut a hole for it in the flooring using a jigsaw.
My question is about the mounting flange that was on the floor specifically regarding the height relative to the toilet.
The toilet has to be removed and the flooring cut to go around the floor drain.
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If the subfloor is unlevel you can fix low spots with a self leveling product and sand or grind down high spots.
Then the toilet is reset so the base covers the cuts around the drain.