Interesting new mods. I have suspected from the first pictures that the 056 should have enough room astern for a TAS, especially when you consider just how disproportionately high the helipad is. They could easily have taken am entire deck off the back and had enough clearance for a proper hanger, so the design choice to forgo that must mean they get something more important in return.
As for the large openings in the back, there are three possibilities that I can think off attomh.
1) It is to provide the crew with some open air recreational space without having to compromise any capabilities to do so. The 056 is after all, a small and compact ship. Where can crew members get some fresh air if the rear was fully enclose? Using the helipad would mean no helos can be parked there, or use the pad at the same time; the walkways amidships should be kept clear so the AShMs and gun turrets could be used at all times; the bow section should also be kept clear so the main gun could be used, and the top of the after superstructure needs to be kept clear so the FL3000 is always available.
2) Since the 056 is designed as a littoral combatant, it is expected to be operating close by disputed islands and shores where there is a high risk of attack from enemy using mall boats of waiting in ambush on islands.
When larger warships operate in such environments, they typically mount additional HMGs throughout the ship to give 360 visual and weapons coverage.
The integrated twin auto cannons amidships were obviously place with just such a situation in mind, and should provide overkill against such targets in the front and side facing vectors, but they do have some blind spots, partically in the rear quadrant of the ship.
You can station guys on the helipad like most USN ships do, but that makes the helipad unavalable for use, and you really don't want anyone on top of the rear superstructure as there is a high likelihood you would need to use the FL3000 missiles.
The openings are in the perfect place to position 2-4 HMGs or just armsmen with rifles to cover those blind spots the auto cannons cannot easily reach.
3) That the openings are required for ventilation. This is really the least likely scenario IMHO, as there shouldn't be anything back there that needs special ventilation, and even if it did, air conditioners should be able to handle it with no problems and there is just no need to design openings.
Personally, I think that a combination of 1) and 2) is the most likely explanation for why the designers went with the openings, and they likely reduced the size of those openings because as they were, they were a big of a hazzard, especially in rough conditions where you can easily see guys at risk of falling off. The large openings probably also didn't do the ship's RCS any favours as radar can quite easily reflect off of the internals and get a big return from all the machinery and complex angling inside.