I found out that my toilet was leaking at the wax seal so i removed the toilet and found out that the toilet flange was cracked. This is a plastic flange in iron pipe. I bought a new replacement flange and was looking at the install video is shows the flange sitting on top of the floor. Mine is level with the floor. Should I (1) install as it was before and send it, (2) install a small piece of 16 gauge metal so it will sit at floor level, (3) Burn the house down?
Assuming I understand your situation, I've had the same issue when I've added tile to a floor. In the cases where I thought the wax ring might leak, I either used the thick one or doubled up a regular one. You could shim up the closet flange, but you'd need to make sure it's secured to the floor/subfloor. 16ga steel might not work long term.
Just went through this not long ago. I got a new plastic flange, mounted it the best I could in the cast iron drain pipe with it being LEVEL above the floor, which the previous owner DID NOT do, and used shims and spacers so that when my 275lbs sat on it and danced it wouldn't move.
Double up wax rings, or find some of the super sized ones. My Lowes sucks and didn't have them, try an Ace or a plumbing supply.