Flooring – underfloor heating and mold forming

Usually 3 zones is plenty for a single story structure of this size. In this case I think your contractor has given you good advice. The distribution is to like living areas which is good. Obviously, more zones allow more flexibility and control, but the costs of equipment and labor rise as more zones are added.

Ecnerwal gave you a VERY good answer, and I'd like to underscore one point in a separate answer ("accept" Ecnerwal's answer, mine's just supplemental).

I have a neighbor who did something similar, laid pipes into a well-sunlit concrete floor. He learned a strong lesson from doing that: while heat RISES through masonry very very well, heat does NOT travel downward through masonry very well at all; you can't count on the blazing-hot upper surface to heat any pipes below it if the pipes are more than one or two inches below the surface. Experiment by (reversibly) peeling up a little of the terrace surface on a blazing hot sunny day, and feel its underside. I think you'll find that if that stone is more than a couple of inches thick, its underside will be easily 50*F cooler than the top surface, and possibly as much as 100*F cooler.

My neighbor never DID get any benefit to his under-floor pipe, so he abandoned it. You, too, may get no measurable benefit. Too, you should know that the long run of pipe may slow down the hot-water flow by virtue of friction.