Do I need to cement board the entire floor and walls, or just water traffic areas like the toilet, tub , and shower?

What is the final surgace going to be. Cement board over a tongue and groove plywood screwed and glued is a great sub for ceramic tile. Don't cut corners to save $30. Wet areas must be concrete board or something like Kerdi board.

The finish will be ceramic tile half way up and then painted

Use cement board on the floor unless it's concrete and at least 6' up from drain in shower area.
I used red guard on my bathroom concrete floor to serve as an isolation membrane.

I don't think you ever told us about your existing sub floor, what is it? You can't install cement board over dimensional lumber so tell us what is there.

I'm replacing the entire floor because of water damage, so the base will be 3/4" plywood flooring over 2x10 floor joist.

I know I need at least some kind of crete backer board, but there's all kinds of sub floor to put in between that and the tile.

At totem when looking at tile they had four different kinds of impact absorbing subfloor for tile.

Go with T&G ply glued and screwed. Your cement board is set in modified thinset and also screwed.

So go with tongue & groove first layer, cement board & thinset second layer, frame tub & shower, moisture barrier cement board & thinset shower & tub frames.

Green board the rest, lay tile and paint?

So go with tongue & groove first layer (glued and screwed), cement board & thinset second layer (and screwed)