A couple of things to chew on. Once that sub is on the surface it is no more stealthy than any other amphib. So the advantage of the sub, if any, may be the ability to show up undetected. Now the question is two fold. One, which sort of force can arrive unannounced and undetected, and two, once there which force can do the job better.
A surface force is not inherently easy to find. There are a number of ways to avoid detection by satellites, the easiest being to simply hide under a weather front and turn all the electronic emitters off. Such "zip lip" ops are routine. Signaling is accomplised by signal light, flags and semiphore, just like the old days. Radars are operated in a passive listening mode, ready to be lit off if a potential threat is detected. Sensor data can be shared in real time over data links. Such digital data transfer is highly directional so there is no way to sense it or to direction find it. The limitation is that it is line of sight. A land base AWACS can give such a force all the radar horizon it needs without ever giving the game away. The presence of an AWACs doesn't necessarily imply a surface force is present and doesn't give away any position information either. It's just an AWACs flying around. Any ship or aircraft in line of sight of each other can share a complete combat picture using a data link and offboard sensors. You can conduct flight ops from any carrier or other air capable ship this way all day as long as there is something resembling VFR conditions under the weather. The ship uses light signals and a person on deck to guide the aircraft to a safe landing. Now with a GPS based approach guidance system the carrier and LHD/LHA at least will be able to conduct instrument approaches without giving it's position away.
When it comes to unloading the force for the assault, the USN has it over every other navy. We can unload the MAF and place it ashore on a hostile beach in six hours flat. Every ship empty in six hours, this is the standard and what is practiced in training. Your notional sub, absent a well deck, LCAC's and large helo force will be hard pressed to match this. The Brits required 48 hours to put two infantry brigades ashore in the Falklands. They had two well deck ships available and a distinct shortage of helo spots to work with. Every ship the US uses now has a well deck and multiple helo spots. Without a big well deck your submarine force will require ages to unload. Where is the gunfire support for the landing force? Where is the umbrella of air defense missiles to protect the aircraft supporting the landing force, and to turn back enemy counterstrikes. The USN relies on AEGIS and Standard Missiles to cover the landing zone with air defense missiles cover until the landing force is established ashore with it's own expeditionary airstrip and protable AAA.
I also have to wonder how you will arrange the various vehicle ramps inside such a ship, not to mention the low flight deck and basic instability of a sub on the surface will make for a very wet flight deck with a lot of motion for the pilots to accomodate. Ever land on a ship in a big swell? That's what I thought. The first time a wave washes over the bow during flight ops you will have a tragedy, and to maintain something resembling pilot and flight deck crew proficiency that sub will need to surface and conduct flight ops frequently. You cannot have such a low freeboard on a flight deck unless you limit it's use to dead calm seas.
The USN gains it's stealth by making it possible to unload the entire force from over the horizon. No ship will be within sight of land. LCAC's make three quarters of the world's shoreline accessible to a landing force. They can traverse marshes that no landing craft could attempt to enter. They can cross dry land and cross obstacles up to two meters high. The forces helos can place other Marines ashore well behind enemy lines. In short you can have Marines popping up at multiple points during an assault while all the ships are out of sight over the horizon. Surprise! And you can conduct this assault in a six hour period. That is how you take your enemy by surprise.
