Tile – Does the side of Hardibacker cement board really matter

You may break a few pieces(of marble) just picking them up.

A skim coat on either side of the joint will help.

Block feather with a concrete 'rubbing' block.

My marble floor always have Schluter Ditra under them. I also use it with any questionable floor.

Ceramic tile can tolerate L/360 deflection, stone is twice as sensitive at L/720.

If you have any doubts about floor springiness, use an isolation membrane or stiffen joists or add a beam. Cement board does little for stiffness.

Consider using high intensity LEDs at the edges. This is how they illuminate light panels in elevators - using some kind of diffusing backing behind it or properly-selected tiles that can be lit from the top or bottom.

The problem with using fiber optics is if they break, you can't service them if they're mortared along with the tile. Light the tile from the edges and the lighting system can be serviced.