Flooring Tile - Alternatives to mud base

Removed old tile and mud base from floors of two bathrooms and need to install new tile. The wall tiles, toilet flanges and and shower curb (in one bath) were originally installed to match a 1.25 inch mud base.

Can I install TWO layers of backer board to achieve the necessary height so that the floor tiles;
1. support the toilet flange?
2. meet the wall and shower curb cove tiles?

The exit lines in this house are 2" thin walled copper and the flange is brass, which is soldered to the exit line.

If you need to raise the floor height do it with a layer of plywood and then backerboard. The backerboard is heavy, expensive, hard to work with, provides relatively no structural support and has to be set in a bed of thinset. Its also not made to be stacked like that for additional height. 3/4" exterior grade bc or better plywood and 1/2" backerboard should get you to approx 1 1/4" or slightly higher (including the thinset under the backerboard).

You could also put a new mud bed in here since you have the height. If you have any leveling or out of plane issues to deal with, a mud bed would solve those as well.