The PEX should probably be sleeved where it passes through the concrete so that it's free to expand and contract with changes in water temperature and pressure.
There's no need to worry about freezing: it's under a heated building, so the ground here will stay above freezing.
Make sure the backfill is done well, meaning that it is compacted well. Don't just dump native soil into the hole and pour concrete over. A sand, small gravel, or road base might be best particularly to provide bedding under the PVC drain pipes. It probably makes sense to fully fill the hole with the same material rather than carry in soil to finish the job.
I don't see any reason why pouring 6" thick would be beneficial, except that it reduces the amount of other fill needed!
I might consider adding dowels. This involves drilling holes horizontally into the surrounding concrete. A "dowel," or short piece of steel rebar, is inserted into each hole so that it's partly in the old concrete and partly exposed to become encased in the new concrete. Dowels help prevent movement at a concrete joint. Here dowels would give you some insurance against future movement of the concrete turning into cracks appearing in your new tile floor. But I'm no expert on this: maybe there's enough surface profile in the broken edges of the old concrete already and dowels would be unnecessary. A tile contractor should be able to give a good assessment.