You cannot use a patching product to "plane/flatten" the floor then install cement board over that. You need the cement board installed first in a bed of fresh thinset THEN after the cement board is contoured to the subfloor you can plane the surface from there.
Overall Self Levelling Compound would be the path of least resistance. It's a great product but requires some attention to detail. To discourage the use of SLC is a sign of inexperience.
Floating floors have nothing to do with this project and shouldn't even be in the conversation.