Bathroom tile once again

I am going to of course wait until I have the downstairs toilet back on and working 100% before we go after the upstairs bathroom but I have a question. Since the old tile upstairs is loose I went ahead and pulled up a few of the 30+ year old tiles and found the same mortar thickness that had been our problem downstairs. It is not in good enough shape for me to leave it and just replace the tiles on top of it so we will end up with the same toilet height problem unless we plan ahead. Would it be best to cut backerboard and lay it at approximately the same height as the old mortar before we start putting down thinset and the new tile? This ceramic tile laying is getting addictive, lol. Thanks for any advice.

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