I'll take a crack at that.
In my '84 MH, the toilet flange is screwed down through the carpet and then through the floor. This is a totally icky arrangement if/when it leaks.
I removed the toilet and hacked the carpet out from underneath the flange. I then installed 1/4" plywood in the whole bathroom, cutting the pieces out to fit under the flange. The tile I used (1'squares, linoleum I assume) filled the rest of the gap under the flange. I installed the new toilet with no issues. It's important to make sure that you close that gap otherwise when you install the toilet you'll be putting a lot of pressure on that flange and therefore the black water tank.
ALTERNATIVELY, some flanges are threaded on. You may be able to wind it down some more or replace it with a new one that will fit flush with the new floor. My flange was glued onto the top of the tank so I had to fill the gap with underlayment and tile before reinstalling the toilet.
My new toilet's fresh water valve sprung a leak and ruined my new floor, so I'll be doing this again in the Spring. Good times.