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Ok, it looks like you have some flange extenders in your second pic. You need to use as many as it takes to build the flange height up so it above the top of the tile. Be sure you use the sealant that comes with them between each one and also the flange. You must clean all the old wax off the flange or the sealant won't bond. Also you must screw the extenders down to the plywood sub floor using stainless steel screws. One screw on each side of the bolt notch on both sides of the extender
Not ok to mortar over the extender. You have to build the flange up with multiple extenders (see attached pic) until the top of the built up flange is higher than the top of the tile. There is no other option. They usually come in a package with several and a tube of adhesive caulk. You can also use the wax from a wax seal to seal between the sections. If there's nothing to screw to you can top all the extenders off with a metal repair ring which will have screw holes i a different place